GST Amnesty Scheme 2026: Notification, Eligibility & Filing Steps

Your clients are sitting on unresolved GSTR-3B defaults, lapsed GSTR-10 filings, and pending annual return obligations — each one a late-fee liability that compounded quietly. The 2026 GST amnesty notification is the government's clearest signal yet to clean up that backlog. Act in the window, or watch those demands land in the next scrutiny cycle.

What the 2026 GST Amnesty Notification Actually Says

The Central Board of Indirect Taxes and Customs (CBIC) periodically issues amnesty notifications under Sec 128 of the CGST Act, 2017, which empowers the government to waive or reduce late fees. The 2026 iteration follows the same statutory route, typically through a gazette notification amending the late-fee structure for specific return types and specific default periods.

According to the official CBIC portal (cbic-gst.gov.in), these notifications cap or fully waive late fees payable under Sec 47 of the CGST Act for returns filed within a specified amnesty window. The corresponding SGST notification — issued by each state government — mirrors the CGST notification, so the combined late-fee relief applies to both heads.

Practical consequence for your desk: Any demand notice issued under Sec 73 or Sec 74 CGST Act that arose purely from non-filing of these returns — not from a tax shortfall — is candidates for resolution through this scheme. If your client has received a GSTR-3A notice (system-generated intimation for non-filers), filing within the amnesty window extinguishes the late-fee component that would otherwise accompany the eventual filing.

Returns Covered: GSTR-3B, GSTR-9, and GSTR-10

The 2026 amnesty scheme, consistent with the pattern established in earlier schemes (including the one announced via Budget 2024 recommendations and operationalised through CBIC Circular No. 238/32/2024-GST), targets three return categories:

Return	Who files it	Default period typically covered	Late fee cap under amnesty
GSTR-3B	All regular taxpayers	FY 2017-18 to FY 2022-23 (check current notification for exact range)	Nil for nil-liability periods; capped at ₹500 (₹250 CGST + ₹250 SGST) for periods with liability
GSTR-9	Taxpayers with turnover above ₹2 crore	FY 2017-18 to FY 2022-23	Waived or reduced per notification
GSTR-10	Taxpayers who have cancelled registration	Final return pending post-cancellation	Reduced to ₹1,000 (₹500 CGST + ₹500 SGST) from the standard ₹10,000 maximum

Always cross-check the exact notification number on cbic-gst.gov.in for the precise financial year range and fee caps applicable to the 2026 window — CBIC amends these details with each new notification, and using the wrong year range is the most common error in amnesty filings.

GST Amnesty Scheme Eligibility 2026: Who Qualifies

This is where most accountants spend too little time. The eligibility filter is straightforward but unforgiving:

You qualify if:

• The return was due but not filed as on the date specified in the notification (usually a cut-off date in the immediately preceding financial year).
• The taxpayer's GSTIN was active during the period the default return relates to.
• The taxpayer files the overdue return within the amnesty window — typically a 3-to-6-month window from the notification date.
• For GSTR-10, the cancellation order has already been processed and the final return is pending.

You do not qualify if:

• The return period falls outside the years specified in the notification. Filing a default GSTR-3B for FY 2023-24 under a notification capped at FY 2022-23 gets no relief.
• Late fees have already been paid in full before the amnesty notification date. There is no refund mechanism for fees already deposited — a fact that creates genuine grievance but is settled law under Sec 54 CGST Act (refund of tax paid in excess does not extend to fees paid in accordance with a valid order).
• The taxpayer has been subjected to a concluded adjudication order under Sec 73/74 where late fee formed part of a confirmed demand. Amnesty notifications typically exclude demands already crystallised by order.
• The GSTIN has been suspended under Rule 21A CGST Rules due to a reason other than non-filing (e.g., suspected fraud).

Edge case to watch: Composition taxpayers filing GSTR-4 are sometimes covered under separate notifications. Do not assume GSTR-3B relief extends to GSTR-4 automatically — check the notification's "Explanation" clause.

The GSTR-10 Late Fee Waiver: A Specific Alert

GSTR-10 defaults are disproportionately large in absolute late-fee terms because the standard maximum is ₹10,000, and many small taxpayers who cancelled registration simply did not know about the final return obligation. The 2026 amnesty brings this down to ₹1,000 — an 90% reduction.

The filing mechanics for GSTR-10 under amnesty are identical to a normal GSTR-10 filing on the GST portal, except the system automatically applies the reduced fee at the time of payment. If the portal is not reflecting the reduced fee, it is usually because:

1. The amnesty window has not yet opened on the portal's backend (CBIC portal activation sometimes lags the gazette notification by a few days).
2. The GSTIN is in a state where the corresponding SGST notification has not yet been issued.

In both cases, wait 48–72 hours and retry before raising a grievance ticket.

Step-by-Step Filing Process Under the Amnesty Window

1. Identify all defaulting GSTINs in your client portfolio. Run a bulk GSTIN status check on the GST portal's taxpayer search. Flag any with "Active – Return Defaulter" or "Cancelled" status with pending GSTR-10.

2. Pull the liability summary. For GSTR-3B defaults, use the GSTR-2A/2B data to reconstruct input tax credit positions for the relevant period before filing. Filing a zero-liability GSTR-3B where liability actually existed creates a larger problem than the late fee itself.

3. Compute the correct late fee. The amnesty notification specifies the maximum fee payable. The system computes ₹50/day (₹25 CGST + ₹25 SGST) up to the notification cap. Do not manually compute; trust the portal's challan generation — but verify the final amount before payment.

4. File the return and pay the fee via PMT-06/cash ledger. There is no separate amnesty application form. Filing the return within the window is itself the claim.

5. Download the filed return acknowledgement (ARN). Archive it against the client file. If a scrutiny notice arrives later citing the same period, the ARN and the fee payment receipt are your first-line defence.

6. Update the compliance tracker. Mark the period closed with the ARN and challan reference. Many firms miss this step, leading to duplicate follow-up work.

Want to test your working knowledge of GST return compliance and late-fee computations? The SuperAccountant skills quiz covers exactly these scenarios with instant feedback.

Common Mistakes That Nullify Amnesty Relief

• Filing the wrong GSTIN. In group company structures, a return filed under the holding company's GSTIN for a period when a subsidiary held its own registration does not qualify.
• Filing after the amnesty window closes. The portal typically enforces this automatically, reverting to the standard late-fee rate. There is no offline or manual waiver process once the window shuts.
• Ignoring state-specific notifications. Two CBIC notifications (CGST + IGST) and one per state (SGST) are required. Most states follow promptly, but a handful have historically delayed. Verify on your state's commercial taxes portal before advising the client that full relief is available.
• Confusing amnesty with penalty waiver. Sec 128 covers late fees under Sec 47. Penalties under Sec 122 or Sec 125 CGST Act are a separate matter and are not covered by these notifications.

Planning Beyond the Amnesty: Building a Clean Compliance Calendar

Amnesty schemes are not a recurring feature — they reflect accumulated system-level defaults, and the government has signalled intent to tighten enforcement as the GST infrastructure matures. The practical lesson is structural: build a monthly compliance dashboard that flags overdue returns at day 1 of default, not day 90.

If you are managing 50+ GSTINs, tools like the GST portal's bulk filing facility, or accounting software with direct GSTN API integration (Tally Prime 4.x, Zoho Books), cut the manual tracking load significantly. The compliance calendar should also account for GSTR-1 versus GSTR-3B sequencing — GSTR-3B for a month cannot be filed before GSTR-1 is filed, a dependency that cascades late fees if the upstream return slips.

For accountants building out advisory practices, the ability to identify and resolve compliance backlogs proactively — rather than reactively after a notice — is a billable differentiator. The amnesty window is, in that sense, also a business development opportunity: reach out to dormant clients with pending GSTINs before they receive a Sec 73 notice and seek help elsewhere.

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