GST Amnesty Scheme 2026: GSTR-10 Late Fee Waiver Guide

If your registration was cancelled and GSTR-10 was never filed — or filed years late — the accumulated late fee can easily run into tens of thousands of rupees, enough to make taxpayers abandon the filing altogether. The 2026 GST Amnesty Scheme targets exactly this group: cancelled registrants sitting on unfiled or belatedly filed GSTR-10 returns with runaway late-fee liability. This post cuts through the headline and tells you what the notification actually requires, what fees you will pay, and how to execute the filing before the window shuts.

What GSTR-10 Is and Why Late Fees Spiral So Fast

GSTR-10 is the final return mandated under Section 45 of the CGST Act, 2017. Every taxpayer whose GST registration is cancelled or surrendered must file GSTR-10 within three months of the cancellation order date or the effective date of cancellation, whichever is later — as prescribed under Rule 81 of the CGST Rules, 2017.

The late fee under Section 47 of the CGST Act is ₹200 per day (₹100 CGST + ₹100 SGST/UTGST), with no statutory upper cap for GSTR-10 under the standard provision. A taxpayer who missed the deadline by two years is therefore staring at approximately ₹1,46,000 in late fees before even opening the portal. That number alone explains why hundreds of thousands of final returns remain unfiled — the liability is so disproportionate to the actual tax dues (which are often nil) that compliance feels irrational.

The 2026 GST Amnesty Notification: Core Terms

The CBIC has issued a notification under Section 128 of the CGST Act — which empowers the government to waive or reduce late fees — extending amnesty relief specifically to GSTR-10. According to the official portal at cbic-gst.gov.in, the scheme caps the late fee for GSTR-10 at ₹1,000 total (₹500 CGST + ₹500 SGST/UTGST) for returns filed within the amnesty window, regardless of how long they have been outstanding.

The key parameters of the 2026 amnesty notification for GSTR-10 are:

Parameter	Standard Position	Amnesty Position
Applicable return	GSTR-10 (Final Return)	GSTR-10 (Final Return)
Governing section for waiver	Sec 128, CGST Act	Sec 128, CGST Act
Normal late fee	₹200/day (no cap)	Capped at ₹1,000 total
CGST component	₹100/day	₹500 (flat)
SGST/UTGST component	₹100/day	₹500 (flat)
Who qualifies	—	Registration cancelled on or before a specified cut-off
Filing window	—	As notified — confirm current dates at cbic-gst.gov.in

Practical consequence: A taxpayer three years overdue pays ₹1,000 instead of ₹2,19,000. That delta is the entire case for acting immediately.

Who Qualifies for the GSTR-10 Late Fee Waiver

Eligibility is not universal. Read these conditions carefully before advising a client or employer:

• Registration status: The GST registration must have been cancelled — either suo motu by the proper officer under Section 29(2) of the CGST Act, or on the taxpayer's application under Section 29(1) — on or before the cut-off date specified in the notification. Verify the exact cut-off on cbic-gst.gov.in.
• GSTR-10 not yet filed or filed late before amnesty window: The scheme covers both (a) taxpayers who have not filed GSTR-10 at all, and (b) those who filed it after the due date but within the amnesty window. If you already filed late and paid the full late fee before this notification, the waiver does not create a refund entitlement — a well-established principle under Section 54 (refund provisions do not apply to fees already discharged).
• Outstanding tax and interest must be paid: The late fee waiver does not extend to tax dues or interest. Any liability in the final return — closing stock ITC reversal under Rule 44 of the CGST Rules, or any output tax liability — must be discharged in full to complete the filing.
• No pending appeal on cancellation: If the cancellation order itself is under challenge before an appellate authority, clarify the status before filing GSTR-10, as filing may be construed as acceptance of the cancellation.

Filing Sequence: Step-by-Step on the GST Portal

Getting the sequence right matters because errors in GSTR-10 cannot be revised once submitted.

1. Log in to GST Portal (gstin.gov.in) using the cancelled taxpayer's credentials — the login remains active even after cancellation for compliance purposes.
2. Navigate to Returns → Final Return (GSTR-10). The system will display the applicable period from the last filed return through the effective cancellation date.
3. Declare closing stock. This is the most consequential part of GSTR-10. Report stock on which ITC was availed and which remains on the date of cancellation. The system auto-calculates the ITC reversal amount — cross-check this against your books in Tally Prime or Zoho Books before submission.
4. Pay ITC reversal and any other tax dues through Form GST PMT-06. Use the Electronic Cash Ledger; the Electronic Credit Ledger is not available for payment after cancellation in most scenarios.
5. Pay the reduced late fee of ₹1,000. The portal will reflect the amnesty-capped amount if you are filing within the notified window. Do not proceed if the portal is still showing the full late fee — raise a ticket or check whether the amnesty notification has been implemented on the backend for your jurisdiction.
6. File with DSC or EVC as applicable. Proprietary firms and individuals can use EVC; companies must use DSC per Rule 26 of the CGST Rules.
7. Download the filed GSTR-10 acknowledgement (ARN). Retain this along with the cancellation order — auditors and banks may ask for it when the entity subsequently starts a new venture.

Common Errors That Derail GSTR-10 Filing

Competitor guides stop at the notification headline. Here is what actually goes wrong at the desk:

• Mismatch in closing stock valuation. The ITC reversal under Rule 44 is calculated on the tax applicable to the transaction value of closing stock, not the cost. A ₹5 lakh closing stock of goods attracting 18% GST means an ITC reversal of ₹90,000 — ignoring this creates a demand later under Section 73 or 74.
• Cancelled registration but GSTR-3B pending for earlier periods. GSTR-10 cannot be filed if prior period returns are outstanding. Clear all pending GSTR-1 and GSTR-3B filings first. This is the most frequent reason taxpayers find the GSTR-10 link greyed out.
• Input Service Distributor or e-commerce registrations. These categories have specific cancellation compliance requirements beyond GSTR-10 — do not assume the amnesty and this filing sequence covers them without checking the specific notification language.
• Composition taxpayers. Their final return is also GSTR-10, but their ITC reversal calculation differs since ITC was never availed. Confirm nil stock disclosure is accurate.

If you want to test your understanding of GST return compliance concepts before working on a live client file, the SuperAccountant quiz covers GSTR-10 scenarios alongside other key compliance areas.

What Happens If You Miss the Amnesty Window

Missing the window does not eliminate the obligation — it just makes it expensive again. The standard late fee meter resumes, and the proper officer can also initiate proceedings under Section 62 of the CGST Act (assessment of non-filers) or Section 63 (best judgement assessment for unregistered persons, applicable post-cancellation in certain fact patterns). A demand raised under these sections carries interest at 18% per annum under Section 50 on top of the tax. The amnesty window is genuinely a one-time economic relief, not a filing deadline extension that simply reschedules the problem.

Reconciling GSTR-10 Closure With Books and Future Registrations

Once GSTR-10 is filed and accepted, the entity's GST compliance record is formally closed. Two downstream actions follow:

• Reverse the GST liability in the books. Pass the ITC reversal entry (Debit: ITC Reversal Expense / Credit: Electronic Cash Ledger / Bank) so the balance sheet does not carry a stale GST credit.
• Note the clean compliance record for future registration. If the promoter or proprietor intends to register a new entity for GST, a clean GSTR-10 filing on the cancelled GSTIN avoids objections during the new registration process. The proper officer has the authority under Rule 9 of the CGST Rules to seek clarification on past compliance history.

Accountants handling multiple such clients should build a tracker: GSTIN, cancellation date, GSTR-10 due date, tax dues amount, amnesty fee payable, and ARN once filed. A simple Excel tracker beats portal-crawling for 20 clients at once.

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