GST Amnesty Scheme 2026: GSTR-3B Late Fee Waiver Guide
CBIC has capped GSTR-3B late fees at ₹500–₹1,000 under the 2026 amnesty scheme. Here is the exact GST Portal navigation path, the QRMP-specific rules, and the one liability the waiver does not touch.
By the SuperAccountant Editorial Team
If your GSTR-3B filings from FY 2017-18 through FY 2023-24 are still pending — or you filed them late and the system is showing a runaway late fee — the CBIC's GST Amnesty Scheme 2026 is your window to close that liability at a fraction of the cost. The catch most articles gloss over: Section 50(1) interest on the outstanding tax is not waived, and QRMP taxpayers have a slightly different compliance path. This post gives you the button-by-button walkthrough so you do not waste a portal session.
What the Amnesty Scheme 2026 Actually Says
The scheme flows from the recommendations of the GST Council and is given effect through CBIC notifications issued under Section 128 of the CGST Act, 2017 — which empowers the government to waive or reduce late fees. According to the official CBIC portal at cbic-gst.gov.in, the 2026 scheme caps late fees for delayed GSTR-3B filing as follows:
| Return / Taxpayer Category | Late Fee Cap (per return) |
|---|---|
| GSTR-3B (Nil liability months) | ₹500 (₹250 CGST + ₹250 SGST) |
| GSTR-3B (Tax payable months) | ₹1,000 (₹500 CGST + ₹500 SGST) |
| GSTR-4 (Composition dealers) | ₹500 per return |
| GSTR-9 / GSTR-9C (Annual return) | Capped at 0.04% of turnover (subject to notification limits) |
The cap applies only to returns for the covered financial years (FY 2017-18 to FY 2023-24). Returns for FY 2024-25 onward attract the standard late fee schedule under Section 47 of the CGST Act.
Critical point: The waiver under Section 128 applies exclusively to the late fee component. Interest accrued under Section 50(1) of the CGST Act on the net tax liability remains fully payable. If you owe ₹80,000 in tax for a missed quarter, you must calculate 18% per annum interest from the due date of GSTR-3B to the actual date of payment — the amnesty does not reduce this by a single rupee.
Who Qualifies: QRMP Taxpayers Pay Attention
Under the Quarterly Return Monthly Payment (QRMP) scheme (applicable to taxpayers with aggregate turnover up to ₹5 crore), returns are filed quarterly but IFF (Invoice Furnishing Facility) is used monthly. The GSTR-3B under QRMP is filed quarterly, not monthly. This has two practical consequences for the amnesty:
- Late fee calculation is per quarterly return, not per month. A QRMP taxpayer who missed three quarters in FY 2022-23 faces a maximum capped late fee of ₹1,000 × 3 = ₹3,000 (assuming tax was payable in each quarter), not ₹1,000 per month.
- PMT-06 challans (the monthly tax payment mechanism for QRMP) do not carry a late fee in isolation — the fee attaches to the quarterly GSTR-3B. Arrears on PMT-06 carry only the Section 50(1) interest exposure.
If you are a monthly filer who crossed the ₹5 crore threshold and moved out of QRMP, you need to verify which periods were filed as quarterly versus monthly before computing your late fee exposure.
Step-by-Step Portal Navigation to File Under the Amnesty
Before you start, keep these ready: your GSTIN login credentials, the list of pending/late-filed GSTR-3B periods, and the computed Section 50(1) interest amount (you will need to pay this via DRC-03 or as part of the GSTR-3B filing itself).
Step 1 — Log in Go to https://www.gst.gov.in → click Login → enter your credentials.
Step 2 — Identify pending returns Navigate to Services → Returns → Track Return Status. Set the Return Filing Period to the relevant financial year. The system will display all GSTR-3B periods with their status: Filed, Not Filed, or Filed Late. Note every "Not Filed" period — these are the ones eligible for the capped fee.
Step 3 — Check your late fee liability Go to Services → Ledger → Late Fee Liability Ledger. The portal auto-populates the late fee outstanding. Under the amnesty, the system should reflect the capped amount once the relevant CBIC notification is operationalised in the backend. If it still shows the uncapped figure, do not file yet — verify on the CBIC portal or the GST helpdesk (1800-103-4786) that the notification has been activated for your return period.
Step 4 — File the pending GSTR-3B Navigate to Services → Returns → Returns Dashboard → select the financial year and return period → click GSTR-3B → Prepare Online (or Prepare Offline if you are uploading from Tally Prime or Zoho Books).
- Fill Table 3 (outward supplies), Table 4 (ITC), and Table 6 (payment of tax) accurately.
- In Table 6.1 (Payment of Tax), include the Section 50(1) interest amount in the Interest column. Do not leave it blank hoping it gets waived — it will not.
- Proceed to Compute Late Fee — the portal will apply the cap automatically if the notification is live.
Step 5 — Make payment Proceed to the Payment section. The challan (PMT-06/PMT-09) will show:
- Tax: your actual liability
- Interest: Section 50(1) amount
- Late Fee: capped amount (₹500 or ₹1,000 depending on nil/non-nil month)
Pay via NetBanking, NEFT/RTGS, or Over-the-Counter as applicable. Save the CIN (Challan Identification Number).
Step 6 — Submit and file Click Submit → verify the summary → click File GSTR-3B → authenticate using EVC (OTP on registered mobile) or DSC. Download the filed return acknowledgement (ARN) immediately.
Step 7 — Verify in Track Return Status Go back to Services → Returns → Track Return Status and confirm the period now shows Filed. This is your compliance evidence — screenshot it and save it against the client file or your own records.
The Section 50 Interest Calculation: Do It Before You File
Many accountants file the return first, then scramble on the interest. Do it the other way. Use this formula:
Interest = Net Tax Liability × 18% × (Days Delayed ÷ 365)
Example: You owe ₹1,20,000 in net GST for Q2 FY 2022-23 (July–September 2022). The GSTR-3B due date for a monthly filer was 20 October 2022. You are filing on 15 July 2026 — a delay of 1,364 days.
Interest = ₹1,20,000 × 18% × (1,364 ÷ 365) = ₹1,20,000 × 0.18 × 3.736 = ₹80,698
Compare that to the capped late fee of ₹1,000. The interest dwarfs the fee. This is precisely why the amnesty's benefit is real but limited — it removes the runaway fee, not the time-value cost of delayed payment.
Note: For QRMP taxpayers, the interest is computed at 18% per annum on the shortfall between the actual liability and the amounts deposited via PMT-06 challans during the quarter, per the clarification aligned with Rule 85 of CGST Rules, 2017.
GSTR-4 and GSTR-9 Late Fee Caps: Quick Checklist
The 2026 amnesty is not limited to GSTR-3B. If you handle composition dealers or annual return compliance, tick these off:
- GSTR-4 (Composition Annual Return): Late fee capped at ₹500 per return (₹250 CGST + ₹250 SGST) for FY 2019-20 to FY 2023-24
- GSTR-9 (Annual Return — Normal Taxpayer): Late fee capped; check the specific notification for the turnover-linked ceiling applicable to your client's slab
- GSTR-9C (Reconciliation Statement): Waiver/cap aligned with GSTR-9 notification; confirm on cbic-gst.gov.in for the exact notification number
- Section 50 interest: Payable in full for all of the above — no exceptions
- ITC reversal risk: If ITC was claimed on invoices for the defaulting period and suppliers had not filed their GSTR-1, revisit Sec 16(2)(c) exposure before filing the belated return
- Deadline compliance: The amnesty window has a defined cut-off date per the CBIC notification — file before it lapses; extensions are not guaranteed
For the most current notification number and exact deadline, check the Notifications section at cbic-gst.gov.in directly. Do not rely on secondary sources for the operative date.
Common Errors That Will Get Your Filing Rejected or Flagged
Mismatch in Table 3.1 vs GSTR-1: If your GSTR-1 for the same period was already filed (even late), ensure Table 3.1 of GSTR-3B aligns. The system will flag large divergences and your filing may be held for scrutiny under Section 61 of the CGST Act.
Leaving interest blank: As noted, Section 50(1) interest is not optional. A GSTR-3B filed with zero interest on a late tax payment is an under-declaration and exposes you to a show-cause notice under Section 73 or 74 depending on the department's interpretation of intent.
Filing the wrong period under QRMP: QRMP filers must select the quarterly period (e.g., "Q2 FY 2022-23: July–September 2022"), not monthly sub-periods. Filing a monthly GSTR-3B under a QRMP-active GSTIN for a covered period will create a compliance mismatch.
Assuming the cap is auto-applied: The portal backend is updated by CBIC in batches post-notification. If you see the uncapped amount in the Late Fee Liability Ledger, wait 24–48 hours after the notification's effective date before proceeding.
Build Amnesty Filing Into Your Monthly Close Checklist
The 2026 amnesty is an opportunity to clean up a category of liability that has been sitting on client balance sheets — and on your own firm's compliance tracker — since the teething years of GST. The practical workflow is: export the pending-return list from Track Return Status, compute Section 50 interest for each period in a spreadsheet, collect payment from the client for both tax and interest, then file in chronological order (oldest first, so ITC reconciliation flows cleanly).
If you want to stress-test your understanding of these portal workflows — and the underlying CGST Act provisions — before you sit across a client, the SuperAccountant practice quiz has scenario-based GST questions that mirror exactly this kind of multi-period compliance situation.
Sharpen your edge with SuperAccountant's next live cohort — small batches, real client workpapers, taught by partners. Details and seats at https://app.superaccountant.in/en/cohort.