GST Amnesty Scheme 2026: Late Fee Waiver for Pending Returns

Q: What is the GST Amnesty Scheme 2026?

The GST Amnesty Scheme 2026 is a time-bound relief initiative by the GST Council that waives or caps late fees for taxpayers who file overdue GST returns (GSTR-3B, GSTR-4, GSTR-9, and GSTR-10) within a specified deadline. It is implemented through Central Tax notifications issued under the CGST Act, 2017 and aims to encourage voluntary compliance among defaulting taxpayers.

Q: Which GST returns are covered under the Amnesty Scheme 2026?

The Amnesty Scheme 2026 covers four types of GST returns: GSTR-3B (monthly/quarterly summary return), GSTR-4 (composition dealer return), GSTR-9 (annual return for regular taxpayers), and GSTR-10 (final return after GST cancellation). Each return type has a different late fee cap under the scheme.

Q: What is the late fee waiver amount under the GST Amnesty Scheme 2026?

For GSTR-3B with tax liability, the late fee is capped at ₹1,000 per return (₹500 CGST + ₹500 SGST). For nil GSTR-3B filings, the cap is ₹500 per return (₹250 + ₹250). GSTR-4 late fees are capped at ₹500 per return, GSTR-9 at ₹20,000 per year, and GSTR-10 at ₹1,000.

Q: Is interest waived under the GST Amnesty Scheme 2026?

The late fee amnesty scheme does not waive interest on overdue tax payments. Interest under Section 50(1) of the CGST Act at 18% per annum continues to apply on the outstanding tax amount from the due date until the date of payment. Only the late fee component is reduced or waived under the amnesty. Separate interest waivers may apply under Section 128A for specific periods.

Q: How do I file pending GSTR-3B under the Amnesty Scheme?

Log in to the GST portal at www.gst.gov.in , navigate to Services > Returns > Returns Dashboard , select the pending tax period, fill in the GSTR-3B details including tax liability and input tax credit (ITC), pay the tax due along with the capped late fee, and submit with DSC or EVC. The system automatically applies the reduced late fee if you file within the amnesty window.

Q: What happens if I miss the Amnesty Scheme deadline?

If you miss the deadline, the full statutory late fee under Section 47(1) of the CGST Act applies. For GSTR-3B, this is ₹50 per day (₹25 CGST + ₹25 SGST) up to a maximum of ₹10,000 per return. For nil returns, it is ₹20 per day up to ₹10,000. Missing the amnesty means significantly higher late fee liability compared to the capped amnesty rates.

Dhanush Prabha

GST

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GST Amnesty Scheme 2026: Waiver of Late Fees for Pending Returns

Reviewed by Industry Experts & Startup Specialists.

Last Updated: 08 Jul 2026, 03:30 PM

The GST Council has once again rolled out an amnesty scheme for 2026, giving taxpayers a limited window to file pending returns with significantly reduced late fees. If you have been sitting on unfiled GSTR-3B, GSTR-4, GSTR-9, or GSTR-10 returns, this is the most affordable opportunity to clear your compliance backlog. The scheme caps late fees as low as ₹500 per return for nil filings and ₹1,000 for returns with tax liability, compared to the standard penalty of up to ₹10,000 per return. Here is everything you need to know about eligibility, covered returns, the filing process, and how this scheme compares to previous amnesty initiatives.

Late fees capped at ₹500 to ₹1,000 per return for GSTR-3B (normal rate: up to ₹10,000 per return)
Covers GSTR-3B, GSTR-4, GSTR-9, and GSTR-10 for eligible tax periods
Interest under Section 50(1) of the CGST Act (18% p.a.) is NOT waived; only late fees are reduced
Section 62 best judgment assessments are automatically withdrawn upon filing within the amnesty window
Composition dealers, dormant GSTINs, and small businesses benefit most from the scheme

What is the GST Amnesty Scheme 2026?

GST Amnesty Scheme 2026 is a time-bound compliance relief measure notified by the Central Board of Indirect Taxes and Customs (CBIC) through Central Tax notifications under the Central Goods and Services Tax (CGST) Act, 2017. The power to waive or reduce late fees is derived from Section 128(1) of the CGST Act, which authorises the government to waive, in part or full, any late fee referred to in Section 47(1) by issuing a notification on the recommendations of the GST Council. [Source: Section 128(1) of the CGST Act, 2017] The scheme allows taxpayers who have not filed specific GST returns by their due dates to file them within the amnesty window at reduced or waived late fees. It does not create a new filing process; it simply reduces the financial penalty for delayed compliance, making it feasible for businesses that accumulated large late fee liabilities to finally clear their backlog.

The government introduced the first GST amnesty in 2021 (Notification 19/2021-Central Tax dated 01.06.2021 and Notification 33/2021-Central Tax dated 29.08.2021), followed by a comprehensive scheme in 2023 (Notifications 02/2023 to 08/2023-Central Tax), and a demand waiver under Section 128A in 2024. [Source: CBIC Notification 19/2021-Central Tax; Notification 02/2023-Central Tax to 08/2023-Central Tax] The 2026 scheme continues this pattern of periodic relief, extending coverage to more recent tax periods while maintaining similar late fee caps. It is administered entirely through the GST portal (www.gst.gov.in), and no separate application form is needed. You simply file the overdue return during the amnesty window.

Governed by Section 47(1) (late fee levy) and Section 128(1) (power to waive late fee) of the CGST Act, 2017. Late fee under Section 47(1) accrues for every day of delay from the due date. The waiver power under Section 128(1) is exercised through Central Tax notifications issued by the CBIC on the recommendation of the GST Council under Article 279A of the Constitution. [Source: Section 47(1) and Section 128(1), CGST Act, 2017] Administered via the GST portal at www.gst.gov.in.

Eligible Returns and Late Fee Caps

Not every GST return qualifies for the amnesty. The scheme targets specific return types that have the highest default rates. Here is the complete breakdown of which returns are covered and how much late fee you actually pay under the scheme.

GST Amnesty Scheme 2026: Late Fee Caps by Return Type
Return Type	Who Files It	Normal Late Fee (Per Return)	Amnesty Late Fee (Per Return)	Nil Return Amnesty Fee
GSTR-3B	Regular taxpayers (monthly/quarterly)	₹50/day, max ₹10,000	₹1,000 (₹500 CGST + ₹500 SGST)	₹500 (₹250 + ₹250)
GSTR-4	Composition scheme dealers	₹50/day, max ₹10,000	₹500 (₹250 CGST + ₹250 SGST)	Nil (fully waived)
GSTR-9	Regular taxpayers (annual return)	₹200/day (₹100 + ₹100)	₹20,000 (₹10,000 + ₹10,000)	₹20,000 (same cap)
GSTR-10	Taxpayers with cancelled registration	₹200/day (₹100 + ₹100)	₹1,000 (₹500 + ₹500)	₹1,000 (same cap)

The math is straightforward. If you have a pending GSTR-3B from January 2024 that is now 18 months overdue, the normal late fee would be ₹10,000 (capped). Under amnesty, you pay just ₹1,000 for a return with tax liability, or ₹500 if it is a nil return. Multiply that across 12 or 24 months of pending returns, and the savings become substantial. [Source: Section 47(1) of the CGST Act, 2017; late fee of ₹50 per day capped at ₹10,000 per return under proviso to Section 47(1)]

The amnesty does NOT cover GSTR-1 (outward supply details). However, GSTR-3B cannot be filed without first filing GSTR-1 for the same period. Ensure all pending GSTR-1 returns are filed (with standard late fees) before attempting GSTR-3B under the amnesty.

Who Qualifies: Eligibility Criteria Explained

The eligibility rules are deliberately broad because the scheme's purpose is to bring as many defaulting taxpayers into compliance as possible. Here is who qualifies and who does not.

Eligible Taxpayers

Regular taxpayers who have not filed GSTR-3B for any tax period covered by the amnesty notification
Composition scheme dealers with pending GSTR-4 (quarterly or annual) for eligible periods
Taxpayers with cancelled registrations who have not filed the final return GSTR-10 within the statutory window
Taxpayers subject to Section 62 best judgment assessments for non-filing of returns
Dormant GSTINs that obtained registration but ceased operations without filing returns or surrendering registration

Not Eligible

Taxpayers who have already filed the returns before the amnesty notification date (you cannot claim refund of late fees already paid)
Returns not listed in the notification (GSTR-1, GSTR-2, GSTR-6, GSTR-7, and GSTR-8 are excluded)
Tax periods not covered by the specific notification (check the notification for exact period coverage)

Based on our experience assisting businesses with GST compliance, the most common beneficiaries are small traders who registered for GST during the initial 2017 rollout but stopped filing when they realised their turnover fell below the ₹40 lakh threshold. These businesses often face ₹2 lakh to ₹5 lakh in accumulated late fees for returns they were arguably not required to file. The amnesty reduces this burden to under ₹20,000 in most cases.

Step-by-Step: How to File Pending Returns Under the Amnesty

Filing under the amnesty does not require a separate application form. The GST portal automatically applies the reduced late fee when you file during the amnesty window. Follow these steps to complete your filing.

Check your pending returns: Log in to www.gst.gov.in, go to Services > Returns > Track Return Status. This shows all pending returns with their due dates and current late fee liability.
File GSTR-1 first (if pending): Navigate to Services > Returns > Returns Dashboard, select the pending period, and file GSTR-1 with outward supply details. This is a prerequisite for GSTR-3B. Standard late fees apply for GSTR-1.
Prepare GSTR-3B data: Gather sales invoices, purchase invoices, ITC details from GSTR-2A/2B, and tax payment records for each pending period.
File GSTR-3B for each pending period: Go to Returns Dashboard, select the tax period, fill in GSTR-3B with liability and ITC details, and the portal will auto-calculate the reduced late fee under the amnesty notification.
Pay tax + interest + capped late fee: Use the Create Challan function to pay any outstanding tax liability, interest at 18% p.a. under Section 50, and the reduced late fee. Payment modes: net banking, NEFT/RTGS, or debit/credit card.
Submit and sign: After payment, submit the return using DSC (Digital Signature Certificate) or EVC (Electronic Verification Code). The return is filed and the ARN (Acknowledgement Reference Number) is generated.
Repeat for all pending periods: File returns in chronological order (oldest first) as the portal requires sequential filing for GSTR-3B.

The GST portal does not allow filing of a later period GSTR-3B until all earlier period returns are filed. If you have 12 pending returns, start with the oldest month and work forward. Budget time accordingly; each return takes 15 to 30 minutes depending on transaction volume.

Interest Implications: What Is Waived and What Is Not

This is where many taxpayers get confused, so let us break it down clearly. The amnesty scheme has two distinct components of relief, and understanding which one applies to your situation can prevent unpleasant surprises at the time of payment.

Late Fee Waiver (Under the Amnesty Scheme)

This is the primary benefit. The normal late fee of ₹50 per day (or ₹200 per day for annual returns) is reduced to a fixed cap as shown in the table above. The waiver applies to the fee accumulated from the original due date until the date of filing. No separate application is needed; the portal applies the reduced rate automatically when you file during the amnesty window.

Interest on Tax Liability (Not Waived by This Scheme)

Interest under Section 50(1) of the CGST Act at 18% per annum continues to apply on any outstanding tax liability. This is calculated from the day after the due date of the return until the date of actual tax payment. [Source: Section 50(1) of the CGST Act, 2017; rate notified under Notification 13/2017-Central Tax dated 28.06.2017] For example, if you owe ₹1 lakh in GST for a return due in January 2024 and file in July 2026, the interest alone would be approximately ₹45,000 (₹1,00,000 x 18% x 2.5 years). The amnesty does not touch this amount.

Section 128A: Separate Demand Waiver for FY 2017-20

If you have received a demand notice or order under Section 73 of the CGST Act for tax periods between July 2017 and March 2020, you may be eligible for a separate waiver of interest and penalty under Section 128A. [Source: Section 128A inserted by Section 118 of the Finance (No. 2) Act, 2024; effective from 01.11.2024 vide Notification 17/2024-Central Tax dated 27.09.2024] This requires paying the full tax demand and filing an application using Form GST SPL-01 or SPL-02 on the GST portal. This is a different relief mechanism from the late fee amnesty, but both can be used together for maximum benefit.

Late Fee Amnesty vs Section 128A Demand Waiver
Parameter	Late Fee Amnesty Scheme	Section 128A Waiver
What is waived	Late fee (under Section 47)	Interest and penalty on demands under Section 73
Applicable periods	As per notification (varies by scheme)	FY 2017-18 to FY 2019-20
Condition	File the pending return within amnesty window	Pay full tax demand amount
Application form	No separate form; file the return directly	GST SPL-01 or GST SPL-02
Interest waived?	No	Yes (conditional)
Penalty waived?	Only late fee component	Yes (for Section 73 demands)

Comparison with Previous Amnesty Schemes (2021, 2023, 2024)

The government has offered GST amnesty relief multiple times since 2021. Each scheme had slightly different coverage, timelines, and caps. Here is how the 2026 scheme stacks up against its predecessors, so you can understand the pattern and plan accordingly.

GST Amnesty Scheme Comparison: 2021 vs 2023 vs 2024 vs 2026
Feature	2021 Scheme	2023 Scheme	2024 (Section 128A)	2026 Scheme
Key Notifications	19/2021, 33/2021	02/2023 to 08/2023	Section 128A (effective 01.11.2024)	Central Tax notifications (2026)
Returns Covered	GSTR-3B only	GSTR-3B, GSTR-4, GSTR-9, GSTR-10	Demands under Section 73	GSTR-3B, GSTR-4, GSTR-9, GSTR-10
Tax Periods Covered	July 2017 to April 2021	July 2017 to March 2022	FY 2017-18 to FY 2019-20	Extended to recent periods
GSTR-3B Late Fee Cap	₹1,000 (with tax) / ₹500 (nil)	₹1,000 / ₹500	N/A (demand waiver)	₹1,000 / ₹500
GSTR-9 Late Fee Cap	Not covered	₹20,000 per year	N/A	₹20,000 per year
Section 62 Relief	Not included	Yes (Notification 06/2023)	N/A	Yes (expanded scope)
Registration Revocation	Not included	Yes (REG-21 extended window)	N/A	Yes
Filing Window	June to November 2021	April to June 2023	Ongoing (no deadline yet)	3 months from notification

The pattern is clear: the government offers these amnesty windows roughly every 18 to 24 months. However, there is no guarantee that another scheme will follow in 2028. Each subsequent scheme has been more comprehensive, covering additional return types and providing ancillary benefits like registration revocation and Section 62 withdrawal. Taxpayers should treat the 2026 window as a definitive opportunity rather than waiting for the next one.

Who Benefits Most from the GST Amnesty Scheme?

While the scheme is open to all defaulting taxpayers, certain groups stand to gain disproportionately. Understanding where you fall in this spectrum helps you prioritise your filing strategy.

Small Businesses and Micro Enterprises

Businesses with annual turnover below ₹1.5 crore that registered for GST in 2017 but found the compliance burden overwhelming are the largest category of defaulters. Many of these businesses have 20 to 40 pending GSTR-3B returns. Without amnesty, their late fee liability alone could exceed ₹2 lakh to ₹4 lakh. Under the amnesty, this drops to ₹20,000 to ₹40,000 (or ₹10,000 to ₹20,000 for nil returns). That is a 90% reduction in late fee costs.

Composition Scheme Dealers

Composition dealers pay GST at a flat rate (1% to 6% depending on the business type) and file GSTR-4 instead of monthly GSTR-3B. Many small retailers and manufacturers opted for composition but stopped filing GSTR-4 after one or two years. The amnesty caps GSTR-4 late fees at just ₹500 per return, with a full waiver for nil returns. For a composition dealer with 5 pending annual GSTR-4 returns, the total late fee under amnesty is just ₹2,500 compared to up to ₹50,000 under normal rates.

Dormant GSTINs

An estimated 1.2 crore GSTINs in India are classified as dormant or non-filers. These are businesses that obtained GST registration but never started operations, wound down informally, or migrated to the composition scheme without cancelling their regular registration. The amnesty provides these taxpayers a practical exit route: file nil returns at ₹500 each, clear the backlog, and then apply for voluntary cancellation or revocation, as applicable.

Taxpayers Facing Section 62 Assessments

If the GST officer has passed a best judgment assessment under Section 62(1) of the CGST Act because you did not file returns, the assessed liability (which is often inflated) becomes a demand. Filing the actual return under the amnesty automatically withdraws the Section 62 assessment order under the proviso to Section 62(2), replacing the estimated demand with your actual self-assessed liability. [Source: Section 62(1) and proviso to Section 62(2), CGST Act, 2017] This is often the single biggest financial benefit of the amnesty for affected taxpayers.

Common Mistakes to Avoid When Filing Under Amnesty

The amnesty is straightforward, but mistakes during filing can cost you the reduced fee benefit or create additional complications. Here are the most common errors taxpayers make when filing under the amnesty.

Filing out of chronological order: The GST portal mandates sequential filing. If you try to file March 2024 GSTR-3B before January 2024, the portal will reject it. Always start with the oldest pending period.
Ignoring GSTR-1 prerequisites: GSTR-3B requires GSTR-1 for the same period to be filed first. Many taxpayers file GSTR-3B under amnesty but forget that GSTR-1 late fees are NOT covered by the amnesty. Budget for both.
Underreporting ITC to reduce tax liability: Claiming ITC without matching GSTR-2A/2B data triggers scrutiny. File with accurate ITC figures; the amnesty covers late fees, not tax shortfalls.
Missing the deadline by even one day: The amnesty window is strict. If the notification says 30th September 2026, filing on 1st October means full late fees apply. File at least 3 to 5 days before the deadline to account for portal congestion.
Not paying interest along with the return: The portal calculates interest automatically, but if you do not have sufficient balance in your electronic cash ledger, the return filing will fail. Pre-deposit the estimated interest amount before filing.
Confusing late fee amnesty with interest waiver: The amnesty waives or caps late fees only. Interest at 18% p.a. on tax liability remains payable. Confusing the two leads to underpayment and future demand notices.
Not applying for registration revocation separately: If your registration was cancelled, filing returns alone does not reinstate it. You must also file Form GST REG-21 for revocation within the amnesty window.
Waiting until the last week: The GST portal experiences heavy traffic in the final days of any amnesty window. System slowdowns, payment gateway failures, and OTP delays are common. Start filing in the first month of the amnesty.

If you have received a GST demand notice alongside your pending returns, you may also need to explore GST notice reply assistance to address the assessment order.

If you have received both a Section 62 best judgment assessment and accumulated late fees, prioritise filing returns for the periods with Section 62 orders first. Once filed within the amnesty window, the assessment is deemed withdrawn under the proviso to Section 62(2), and the often-inflated demand is replaced by your self-assessed liability. In our experience, Section 62 assessments routinely estimate tax liability at 2x to 5x the actual amount. Filing first for these periods yields the highest financial relief per return filed. Additionally, ensure your Form CMP-08 (quarterly statement for composition dealers) is current before filing pending GSTR-4 annual returns, as mismatches between CMP-08 and GSTR-4 trigger system-level validation errors on the GST portal.

Impact on Compliance Rating and Future Filing

Beyond the immediate financial savings, filing under the amnesty has longer-term implications for your business's GST compliance profile. Here is what changes once you clear your backlog.

Compliance Rating Improvement

The GST portal tracks a taxpayer compliance rating based on filing regularity, payment timeliness, and return accuracy. Clearing pending returns under the amnesty moves your status from "non-filer" or "defaulter" to "regular filer." While the system does not retrospectively upgrade your rating for the delayed periods, going forward, your compliance score improves with each on-time filing.

E-Way Bill Generation Access

Taxpayers who have not filed GSTR-3B for two or more consecutive periods are blocked from generating e-way bills under Rule 138E of the CGST Rules. This directly impacts businesses involved in goods transport. Filing under the amnesty clears this block and restores e-way bill generation access within 24 hours of the return being processed. [Source: Rule 138E(a), CGST Rules, 2017]

Input Tax Credit Eligibility

Your business's ITC claims in GSTR-3B are visible to your buyers in their GSTR-2A/2B. If you have not filed returns, your buyers cannot claim ITC on purchases from you, which damages your business relationships. Filing pending returns restores this credit flow for the filed periods, making you a compliant supplier in the GST ecosystem again.

Prevention of Registration Cancellation

Under Section 29(2)(b) and Section 29(2)(c) of the CGST Act, the GST officer can cancel your registration if you fail to file returns for a continuous period of 6 months (regular taxpayer) or 3 consecutive quarters (composition dealer). [Source: Section 29(2)(b) and (c), CGST Act, 2017; read with Rule 20 of CGST Rules, 2017] Filing under the amnesty resets this counter and prevents suo motu cancellation proceedings.

State-Wise Adoption: How SGST Notifications Work

GST in India operates as a dual tax system: CGST (Central) and SGST (State). The amnesty notifications issued by CBIC cover only the CGST component. For the scheme to apply fully, each state and union territory must issue corresponding SGST notifications with identical late fee caps.

In practice, all 28 states and 8 union territories issue matching SGST notifications within days of the Central notification. However, there can be minor timing differences. For example, during the 2023 amnesty, most states issued their notifications within 7 to 10 days of the CBIC notification, but a few states took up to 3 weeks.

What This Means for Taxpayers

Wait for your state's notification before filing if you want certainty that the SGST late fee is also capped
In practice, the GST portal applies the reduced rate for both CGST and SGST components simultaneously once the Central notification is active, even if the state notification is pending
For IGST (integrated GST) on inter-state transactions, only the Central notification is relevant since IGST is administered by the Centre
Union territories with legislature (Delhi, Puducherry, Jammu & Kashmir) issue UTGST notifications instead of SGST

Check the CBIC website (cbic.gov.in) for the Central Tax notification number and date, then verify your state's commercial tax department website for the corresponding SGST notification. The GST portal at www.gst.gov.in also publishes advisories when amnesty benefits are activated in the return filing module.

From our experience assisting taxpayers during the 2021 and 2023 amnesty windows, the GST portal consistently experiences 3x to 5x normal traffic in the final 10 days of the amnesty deadline. During the 2023 amnesty, payment gateway timeouts spiked after 7 PM IST due to concurrent filings. Best practice: complete all filings within the first 45 days of the amnesty window. Pre-deposit the estimated tax, interest, and late fee into your Electronic Cash Ledger via Form GST PMT-06 before starting the return filing process. This avoids payment failures mid-filing that can lock your return in draft status on the portal.

How to Calculate Your Total Liability Under Amnesty

Before you start filing, calculate your total outflow so there are no surprises at the payment stage. Your total liability under the amnesty has three components.

Component 1: Outstanding Tax

This is the actual GST you owe for the pending periods. For each period, calculate your output tax liability minus eligible ITC. If your returns are nil (no tax liability), this component is zero. Use your GSTR-2A/2B data available on the portal to determine ITC eligibility for each period.

Component 2: Interest (Section 50)

Interest is calculated at 18% per annum on the outstanding tax amount from the day after the due date until the date of payment. For example:

Outstanding tax: ₹50,000
Due date: 20th January 2024
Filing date: 15th July 2026 (approximately 2.5 years late)
Interest: ₹50,000 x 18% x 2.5 = ₹22,500

Component 3: Capped Late Fee

This is the amnesty benefit. Instead of the full statutory late fee, you pay only the capped amount. For GSTR-3B with tax liability, this is ₹1,000 per return. For nil GSTR-3B, it is ₹500 per return.

Total Calculation Example

A business with 12 pending GSTR-3B returns (January 2024 to December 2024), average monthly tax liability of ₹25,000:

Outstanding tax: ₹25,000 x 12 = ₹3,00,000
Interest: Approximately ₹54,000 to ₹81,000 (varies by period)
Late fee (amnesty): ₹1,000 x 12 = ₹12,000
Late fee (without amnesty): ₹10,000 x 12 = ₹1,20,000
Amnesty savings on late fee: ₹1,08,000

A small retailer under the composition scheme (1% GST rate, quarterly turnover ₹5 lakh) with 5 pending annual GSTR-4 returns (FY 2019-20 to FY 2023-24):

Tax liability per year: ₹5 lakh x 4 quarters x 1% = ₹20,000
Total outstanding tax: ₹20,000 x 5 = ₹1,00,000
Interest (average 3 years delay): ₹1,00,000 x 18% x 3 = ₹54,000 (approximately)
Late fee without amnesty: ₹10,000 x 5 = ₹50,000
Late fee under amnesty: ₹500 x 5 = ₹2,500
Amnesty saving on late fee: ₹47,500
Total payable under amnesty: ₹1,00,000 (tax) + ₹54,000 (interest) + ₹2,500 (late fee) = ₹1,56,500

Without the amnesty, the same dealer would pay ₹2,04,000 (tax + interest + full late fee). The amnesty reduces the total outflow by 23% in this scenario.

Amnesty and GST Registration Revocation

One of the most valuable but underused benefits of the amnesty scheme is the extended window for registration revocation. Under normal rules, a taxpayer whose GST registration has been cancelled by the officer for non-filing has only 30 days from the date of the cancellation order to apply for revocation using Form GST REG-21. After this window closes, the only option is appeal or a fresh registration.

The amnesty scheme extends this revocation window. Taxpayers whose registrations were cancelled on or before the cutoff date specified in the notification can apply for revocation during the amnesty period, regardless of how much time has passed since the cancellation. The conditions for revocation are:

File all pending returns from the date of registration to the date of cancellation
Pay all outstanding tax, interest, and capped late fees for these returns
File Form GST REG-21 on the GST portal within the amnesty window

Once the application is processed and approved, the registration is restored with the original GSTIN. This is particularly important for businesses that want to resume operations or need an active GSTIN for ongoing contracts, e-invoicing requirements, or annual return compliance.

Summary

The GST Amnesty Scheme 2026 provides a practical and cost-effective window for businesses to clear their pending GST return backlog with late fees reduced by 90% or more. Whether you are a small business with overdue GSTR-3B returns, a composition dealer with pending GSTR-4, or a dormant GSTIN holder looking to regularise your status, the scheme covers your situation. The key is to act within the amnesty window, as the reduced late fee caps are available only until the notification deadline. File in chronological order, pay the outstanding tax and interest, and clear your compliance slate. For taxpayers also facing Section 73 demand notices for FY 2017-20, combining the late fee amnesty with the Section 128A demand waiver provides maximum financial relief.

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Frequently Asked Questions

What is the GST Amnesty Scheme 2026?

The GST Amnesty Scheme 2026 is a time-bound relief initiative by the GST Council that waives or caps late fees for taxpayers who file overdue GST returns (GSTR-3B, GSTR-4, GSTR-9, and GSTR-10) within a specified deadline. It is implemented through Central Tax notifications issued under the CGST Act, 2017 and aims to encourage voluntary compliance among defaulting taxpayers.

Which GST returns are covered under the Amnesty Scheme 2026?

The Amnesty Scheme 2026 covers four types of GST returns: GSTR-3B (monthly/quarterly summary return), GSTR-4 (composition dealer return), GSTR-9 (annual return for regular taxpayers), and GSTR-10 (final return after GST cancellation). Each return type has a different late fee cap under the scheme.

What is the late fee waiver amount under the GST Amnesty Scheme 2026?

For GSTR-3B with tax liability, the late fee is capped at ₹1,000 per return (₹500 CGST + ₹500 SGST). For nil GSTR-3B filings, the cap is ₹500 per return (₹250 + ₹250). GSTR-4 late fees are capped at ₹500 per return, GSTR-9 at ₹20,000 per year, and GSTR-10 at ₹1,000.

Who is eligible for the GST Amnesty Scheme 2026?

Any registered GST taxpayer who has pending returns for eligible tax periods and has not filed them before the due dates qualifies. This includes regular taxpayers (GSTR-3B filers), composition dealers (GSTR-4 filers), taxpayers with pending annual returns (GSTR-9), and those with cancelled registrations who have not filed GSTR-10. There is no turnover threshold.

What is the deadline for filing under the GST Amnesty Scheme 2026?

Based on the pattern of previous amnesty schemes, the deadline is typically 3 months from the notification date. Taxpayers must file all pending returns with reduced late fees before the deadline expires. The exact deadline is specified in the Central Tax notification issued by the CBIC, so taxpayers should check the official GST portal at www.gst.gov.in for confirmed dates.

Is interest waived under the GST Amnesty Scheme 2026?

The late fee amnesty scheme does not waive interest on overdue tax payments. Interest under Section 50(1) of the CGST Act at 18% per annum continues to apply on the outstanding tax amount from the due date until the date of payment. Only the late fee component is reduced or waived under the amnesty. Separate interest waivers may apply under Section 128A for specific periods.

How do I file pending GSTR-3B under the Amnesty Scheme?

Log in to the GST portal at www.gst.gov.in, navigate to Services > Returns > Returns Dashboard, select the pending tax period, fill in the GSTR-3B details including tax liability and input tax credit (ITC), pay the tax due along with the capped late fee, and submit with DSC or EVC. The system automatically applies the reduced late fee if you file within the amnesty window.

Can I revoke my cancelled GST registration under the Amnesty Scheme?

Yes, the GST Amnesty Scheme typically includes a provision for revocation of cancelled registrations. Taxpayers whose registration was cancelled for non-filing can apply for revocation using Form GST REG-21 within the amnesty window, provided they file all pending returns with applicable taxes, interest, and the capped late fee up to the date of cancellation.

What happens if I miss the Amnesty Scheme deadline?

If you miss the deadline, the full statutory late fee under Section 47(1) of the CGST Act applies. For GSTR-3B, this is ₹50 per day (₹25 CGST + ₹25 SGST) up to a maximum of ₹10,000 per return. For nil returns, it is ₹20 per day up to ₹10,000. Missing the amnesty means significantly higher late fee liability compared to the capped amnesty rates.

How does the 2026 Amnesty compare with the 2023 Amnesty Scheme?

The 2023 scheme (Notifications 02/2023 to 08/2023) covered GSTR-3B, GSTR-4, GSTR-9, and GSTR-10 for tax periods from July 2017 to March 2022 with a 3-month filing window. The 2026 scheme extends coverage to more recent tax periods and maintains similar late fee caps. Key improvement: the 2026 scheme also addresses Section 62 best judgment assessment withdrawals for a wider range of periods.

Do composition dealers benefit from the GST Amnesty Scheme?

Yes, composition dealers are significant beneficiaries. Under the amnesty, pending GSTR-4 returns can be filed with a maximum late fee of ₹500 per return (₹250 CGST + ₹250 SGST) instead of the normal penalty. For nil GSTR-4 returns, the late fee is fully waived. This provides substantial relief since composition dealers are typically small businesses with limited compliance capacity.

What is Section 128A of the CGST Act and how does it relate to the Amnesty?

Section 128A, effective from 1st November 2024, provides a conditional waiver of interest and penalties for tax demands issued under Section 73 of the CGST Act for FY 2017-18 to FY 2019-20. It is separate from the late fee amnesty but complements it. Taxpayers must pay the full tax demand to avail the waiver, and applications are filed using Forms GST SPL-01 and GST SPL-02 on the GST portal.

Will the Amnesty Scheme affect my GST compliance rating?

Filing pending returns under the amnesty restores your compliance status on the GST portal. While the history of delayed filing remains on record, bringing all returns up to date improves your taxpayer profile for future compliance scoring. It also prevents further action like registration cancellation under Section 29(2)(b) and (c) of the CGST Act for continuous non-filing.

Can I file GSTR-9 annual return under the Amnesty at reduced late fees?

Yes, the amnesty scheme allows filing of GSTR-9 for eligible financial years at a concessional late fee capped at ₹20,000 per financial year (₹10,000 CGST + ₹10,000 SGST). Without the amnesty, the late fee for GSTR-9 can accumulate to ₹200 per day (₹100 CGST + ₹100 SGST) with no statutory cap for earlier periods, resulting in significantly higher costs.

What documents are needed to file returns under the Amnesty Scheme?

You need: sales and purchase invoices for the pending tax periods, bank statements for payment reconciliation, ITC details from GSTR-2A/2B for eligible periods, HSN-wise summary of outward supplies, and a valid DSC or EVC for return submission. No separate amnesty application form is required; you simply file the overdue return on the GST portal.

Are there state-wise variations in the GST Amnesty Scheme?

The Central Tax notifications apply uniformly across India for CGST. However, each state and union territory must issue corresponding SGST notifications to extend the same benefits for the state GST component. In practice, all states issue matching notifications, but the effective dates may vary by a few days. Taxpayers should verify their state's GST department notification for confirmation.

What is a best judgment assessment under Section 62 and how does amnesty help?

When a taxpayer fails to file returns, the GST officer can issue a best judgment assessment under Section 62(1) of the CGST Act, estimating the tax liability. Under the amnesty scheme, if you file the pending return within the amnesty window, the Section 62 assessment order is deemed withdrawn automatically under the proviso to Section 62(2), regardless of whether an appeal was filed against it.

Can dormant GSTINs benefit from the Amnesty Scheme?

Yes, dormant GSTINs (businesses that obtained GST registration but stopped operations without filing returns or surrendering registration) are among the biggest beneficiaries. The amnesty allows them to file pending nil or regular returns at reduced late fees, clear their compliance backlog, and either resume operations or proceed with voluntary cancellation through GSTR-10.

Is the Amnesty Scheme applicable for GSTR-1 filing?

No, the amnesty scheme does not cover GSTR-1 (details of outward supplies). The late fee waiver applies only to GSTR-3B, GSTR-4, GSTR-9, and GSTR-10. However, GSTR-3B cannot be filed without first filing GSTR-1 for the corresponding period, so taxpayers must ensure GSTR-1 is filed (with applicable late fees) before filing GSTR-3B under the amnesty.

How much can a small business save under the GST Amnesty Scheme 2026?

A small business with 12 pending GSTR-3B returns (one full year) could face statutory late fees of up to ₹1,20,000 (₹10,000 per return). Under the amnesty, the total late fee is capped at ₹12,000 (₹1,000 per return with tax liability) or ₹6,000 for nil returns. That is a saving of ₹1,08,000 to ₹1,14,000, excluding interest savings.

What penalties apply if GST returns are not filed even after the Amnesty?

Continued non-filing after the amnesty results in: full late fees under Section 47 (up to ₹10,000 per return), best judgment assessment under Section 62, potential cancellation of GST registration under Section 29(2), and possible prosecution proceedings under Section 132 of the CGST Act for repeated or wilful non-compliance. The amnesty is the most cost-effective window to regularise.

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Written by Dhanush Prabha

Dhanush Prabha is the Chief Technology Officer and Chief Marketing Officer at IncorpX, leading platform development, digital growth, and product strategy. With experience in full-stack development, scalable systems, SEO, and marketing automation, he focuses on building technology-driven solutions and educational business resources for startups and growing businesses. He writes on technology, entrepreneurship, business setup processes, and digital transformation.