The GST late fee for a late GSTR-3B or GSTR-1 is ₹50 a day (₹25 under CGST and ₹25 under SGST), or ₹20 a day for a nil return, until it reaches a cap set by your turnover (a flat ₹500 for a nil return). This guide explains how the portal counts the fee and the 18% interest, how to pay both, what the 57th GST Council proposal would change, and what else a late return blocks. The late fee stops at its cap, but interest on tax paid late in cash keeps running until you pay.
How is the GST late fee counted?
The GST portal counts the days from the due date to the date you actually file and multiplies them by ₹25 a day under each of CGST and SGST (₹10 each for a nil return). The fee is worked out on the filing date, so every extra day adds ₹50 until your cap is reached. There is no late fee under IGST or cess.
A few rules decide the number:
- Section 47 of the CGST Act allows ₹100 a day per Act, up to ₹5,000. Notifications waive everything above ₹25 a day (Notification 76/2018 for GSTR-3B, 4/2018 for GSTR-1) and set lower caps for tax periods from June 2021 (Notifications 19/2021 and 20/2021).
- The cap depends on your aggregate turnover in the previous financial year, not the year you are filing for.
- A GSTR-3B is nil when the central tax payable in it is nil. A GSTR-1 is nil when you made no outward supplies in the period.
- GSTR-1 and GSTR-3B are separate obligations, so a month where both are late carries two late fees, each with its own cap.
Worked example: GSTR-3B filed 25 days late
Bluepeak Foods Private Limited (a made-up company) files monthly and had aggregate turnover of ₹1.2 crore in FY 2025-26. Its GSTR-3B for August 2026 was due on 20 September 2026 and was filed on 15 October 2026, 25 days late. It owed ₹3,00,000 of tax, set off ₹2,20,000 from input tax credit and paid ₹80,000 in cash when it filed.
| Item | Working | Amount |
|---|---|---|
| Late fee under CGST | ₹25 × 25 days | ₹625 |
| Late fee under SGST | ₹25 × 25 days | ₹625 |
| Interest | ₹80,000 × 18% × 25 ÷ 365 | ₹986 |
| Total | ₹2,236 |
The cap for its band is ₹1,000 per Act, so the fee would have kept growing until day 40 and then stopped at ₹2,000. Had the company paid the whole ₹3,00,000 in cash, interest would have been ₹3,699 instead of ₹986.
How does rule 88B reduce interest on late GST payment?
When you file a late GSTR-3B for the supplies of that same period, interest at 18% a year under section 50(1) runs only on the tax you pay from the electronic cash ledger, for the days of delay. Tax set off from input tax credit carries no interest. The relief is lost if the return is filed after proceedings under section 73, 74 or 74A have started for that period.
The relief comes from the proviso to section 50 and rule 88B(1), inserted by Notification 14/2022-Central Tax. Since 10 July 2024, cash credited to the electronic cash ledger by the due date and left there until you file is also kept out of the interest (proviso to rule 88B(1), Notification 12/2024-Central Tax). Two other cases work differently:
- Tax of an earlier period that you pay in a later return carries interest on the full unpaid amount, from the day after it was due until the day you pay (rule 88B(2)).
- Input tax credit wrongly availed and utilised carries interest under section 50(3) from the date of utilisation until it is reversed or paid (rule 88B(3)).
What a late GSTR-9 costs in practice
For FY 2022-23 onwards, the GSTR-9 late fee for aggregate turnover up to ₹5 crore is ₹50 a day in total, capped at 0.04% of turnover in the state. Because the cap is a percentage of turnover, the fee usually keeps growing for months before it stops.
Example. A trader with aggregate turnover of ₹3.2 crore for FY 2025-26, all in one state, must file GSTR-9 by 31 December 2026. Filing on 31 March 2027, 90 days late, costs ₹50 × 90 = ₹4,500. The cap is 0.04% of ₹3.2 crore, or ₹12,800, which it would reach only after 256 days.
The turnover band uses aggregate turnover for the year of the return, while the cap uses turnover in the state of that registration. Two points push the fee up. The GST portal will not accept GSTR-9 until every GSTR-1 and GSTR-3B of that year is filed, so a backlog of monthly returns delays the annual return too. And if turnover exceeds ₹5 crore, the self-certified reconciliation statement in GSTR-9C goes with GSTR-9 (rule 80(3)).
How to pay the late fee on the GST portal
You do not pay the GSTR-3B late fee separately. The portal works out the fee from your filing date, includes it in the late GSTR-3B, and accepts payment only from the late fee head of the electronic cash ledger. Input tax credit cannot be used for the late fee or for interest.
- Go to Services, Returns, Returns Dashboard, select the period and click Prepare Online on the GSTR-3B tile.
- Fill in the tables and check table 5.1 (interest and late fee).
- Click Proceed to Payment and check the cash needed under the tax, interest and late fee heads.
- If the cash ledger is short, create a challan and pay it.
- Click Make Payment/Post Credit to Ledger, then file with DSC or EVC.
File on the day you pay. The fee is computed on the filing date, so a one-day gap can add another ₹50.
Will the 57th GST Council late fee relief cover your return?
Not yet. On 8 October 2026 the 57th GST Council recommended waiving the late fee on returns under section 39(1) for taxpayers with turnover up to ₹5 crore in the preceding financial year, if the late return is filed by the end of the month in which it was due. As of October 2026 it is a proposal, and the normal fee applies until CBIC notifies it.
Read the Council press release closely before relying on it:
- The return under section 39(1) is GSTR-3B (rule 61). GSTR-1 is furnished under section 37 and the composition GSTR-4 under section 39(2), so the recommendation as worded does not name them.
- It covers the late fee only. Interest at 18% on tax paid late would still apply.
- If notified in this form, a September 2026 GSTR-3B due on 20 October 2026 and filed by 31 October 2026 would carry no late fee. Filed in November, it would not qualify.
What else does a late GST return block?
A late GSTR-3B stops you from filing the next GSTR-1, can block e-way bills, and holds up the annual return. After three years from its due date, a return cannot be filed at all under section 39(11).
- Under rule 59(6), you cannot file GSTR-1 or use the invoice furnishing facility while the GSTR-3B for the preceding month or quarter is pending.
- If GSTR-3B or CMP-08 is not filed for two or more consecutive tax periods, your GSTIN is blocked for e-way bills. It unblocks automatically once the default falls below two periods, or you can apply in FORM GST EWB-05. Check when you need an e-way bill with the e-invoice and e-way bill checker.
- For returns past the three-year limit, the GST portal has an application for unbarring returns to the tax officer.
Common mistakes with GST late fees
Most excess GST late fees come from timing and classification errors rather than the rates.
- Using the current year's turnover to pick the cap. GSTR-1 and GSTR-3B caps use the previous financial year.
- Marking GSTR-3B as nil when some central tax is payable, which applies the ₹20 rate wrongly.
- Planning to pay the fee from input tax credit. Only cash is accepted.
- Forgetting that GSTR-1 has its own late fee alongside GSTR-3B.
- Waiting for a waiver. Past amnesties had fixed filing windows, and interest keeps running while you wait.
- Relying on a remembered due date. Check the GST return due dates calendar and the portal for extensions.
If monthly deadlines are the problem, see whether quarterly filing or the composition scheme suits your business. For TDS returns, the TDS late fee and interest calculator works out the separate income-tax fee.
How Ofin can help
Ofin's outsourced accounting team tracks your due dates and prepares and files GSTR-1, GSTR-3B and GSTR-9 for a fixed fee. We reconcile input tax credit before each return, file backlogs in the right order (each GSTR-3B before the next GSTR-1), and check the late fee and interest the portal computes. For a new business, start with GST registration from ₹1,499.
