The GST late fee on a delayed GSTR-3B or GSTR-1 is ₹50 for each day of delay (₹25 under the CGST Act and ₹25 under the State or UT GST Act), or ₹20 a day for a nil return. It stops growing at a cap fixed for each return: ₹500 for a nil return, and ₹2,000, ₹5,000 or ₹10,000 for other returns depending on the previous year's aggregate turnover. The annual return in GSTR-9 runs on its own scale of ₹50 to ₹200 a day, capped by reference to the turnover in the State.
Three rules sit behind every GST late fee calculation. Each return carries its own fee. The fee can be paid only from the electronic cash ledger. And it is charged in addition to any interest on tax paid late. The rates and caps below were checked against the CGST Act and the waiver notifications as on 12 November 2026.
Late fee per return at a glance
Read the two money columns together. The fee for one return is the per-day amount multiplied by the days of delay, or the cap, whichever is lower. Both columns give the combined amount; half is levied under the CGST Act and half under the State or UT law.
| Return and class of taxpayer | Per day of delay | Maximum for one return |
|---|---|---|
| GSTR-3B with nil central tax payable | ₹20 | ₹500 |
| GSTR-3B, aggregate turnover up to ₹1.5 crore in the preceding year | ₹50 | ₹2,000 |
| GSTR-3B, turnover above ₹1.5 crore and up to ₹5 crore | ₹50 | ₹5,000 |
| GSTR-3B, turnover above ₹5 crore | ₹50 | ₹10,000 |
| GSTR-1 with no outward supplies in the period | ₹20 | ₹500 |
| GSTR-1, turnover up to ₹1.5 crore / ₹1.5 crore to ₹5 crore / above ₹5 crore | ₹50 | ₹2,000 / ₹5,000 / ₹10,000 |
| GSTR-4 (composition annual return) with nil tax payable | ₹20 | ₹500 |
| GSTR-4, other cases | ₹50 | ₹2,000 |
| GSTR-9, aggregate turnover up to ₹5 crore in that financial year | ₹50 | 0.04% of turnover in the State or UT |
| GSTR-9, turnover above ₹5 crore and up to ₹20 crore | ₹100 | 0.04% of turnover in the State or UT |
| GSTR-9, turnover above ₹20 crore | ₹200 | 0.5% of turnover in the State or UT |
The portal charges no late fee under the IGST head or on compensation cess. Its manual for filing GSTR-3B says there is no late fee payable for IGST and cess, and those fields are disabled.
How section 47 and the waiver notifications fit together
Most of the figures in the table do not appear in the Act itself. Section 47 of the CGST Act sets a much higher base. Anyone who misses the due date for GSTR-1 (section 37), a return under section 39, the final return under section 45 or the TCS statement under section 52 pays ₹100 for every day the failure continues, up to ₹5,000. For the annual return, sub-section (2) charges ₹100 a day up to 0.25% of the turnover in the State or Union territory. Those amounts are under the CGST Act alone, and each State's GST Act levies a matching fee.
The Central Government then waives everything above a lower figure, using its power under section 128. The table is what remains after those waivers:
- GSTR-3B. Notification 76/2018-Central Tax waives the part of the fee above ₹25 a day, or ₹10 a day where the central tax payable is nil. Notification 19/2021-Central Tax added caps of ₹250, ₹1,000 and ₹2,500 under the CGST Act for tax periods from June 2021. Taxpayers above ₹5 crore have no special cap, so the statutory ₹5,000 applies.
- GSTR-1. Notification 4/2018-Central Tax sets the same ₹25 and ₹10 daily figures, the lower one applying when there are no outward supplies. Notification 20/2021-Central Tax adds the same three caps from June 2021.
- GSTR-4. Notification 73/2017-Central Tax brings the daily fee down to ₹25, or ₹10 where the tax payable is nil. Notification 21/2021-Central Tax caps it at ₹250 for a nil return and ₹1,000 otherwise from FY 2021-22. When the annual return falls due is covered in the GST composition scheme guide.
- GSTR-9. Notification 07/2023-Central Tax applies from FY 2022-23. It cuts the fee to ₹25 a day for turnover up to ₹5 crore and ₹50 a day between ₹5 crore and ₹20 crore, both capped at 0.02% of the turnover in the State or UT. Above ₹20 crore, the statutory ₹100 a day and 0.25% cap still apply.
The amounts in each notification are under the CGST Act, which is why the table doubles them. The GST Council's press release after its 43rd meeting on 28 May 2021 stated the combined caps the same way, for example ₹2,000 per return (₹1,000 CGST and ₹1,000 SGST) for turnover up to ₹1.5 crore.
Two different turnover tests decide the band. For GSTR-3B and GSTR-1 the notifications use aggregate turnover in the preceding financial year, so the August 2026 return is banded on FY 2025-26 turnover. For GSTR-9 the band uses aggregate turnover in the financial year the return covers, while the percentage cap is worked on the turnover of that GSTIN's State or UT. A company registered in four States therefore has four different GSTR-9 caps.
Counting the days of delay
The portal's manual gives the formula: date of filing minus due date of filing, multiplied by the daily rate. A GSTR-3B due on 20 September and filed on 4 November is 45 days late. Filing on the due date itself attracts nothing.
The due dates that start the count are in the rules. Under Rule 61 of the CGST Rules, a monthly GSTR-3B is due on the 20th of the following month. Quarterly filers under the QRMP scheme file by the 22nd or 24th of the month after the quarter, depending on the State. Rule 80 fixes 31 December after the financial year for GSTR-9, and for GSTR-9C where turnover exceeds ₹5 crore.
Two points catch people out. First, the cap applies return by return, so three missed months mean three fees, each with its own cap. Second, delays cascade. Section 39(10) bars a GSTR-3B for a tax period if any earlier return, or the GSTR-1 for that same period, has not been furnished. A late GSTR-1 therefore holds up that month's GSTR-3B, and both fees run together.
Worked examples with 2026 due dates
Illustration. The businesses below are hypothetical and file monthly unless stated. Each total shows the CGST half and the matching SGST half.
One late GSTR-3B with tax payable
A trader with FY 2025-26 aggregate turnover of ₹3.2 crore files the August 2026 GSTR-3B, due on 20 September 2026, on 4 November 2026. That is 45 days at ₹25, or ₹1,125 under each Act, well inside the ₹2,500 cap. The total late fee is ₹2,250.
Had the same return gone in on 30 December 2026, the delay would be 101 days. At ₹25 a day the CGST fee would be ₹2,525, so the cap of ₹2,500 takes over and the total is fixed at ₹5,000 however much later the return is filed.
A nil GSTR-3B filed late
A business with no sales and no tax payable for June 2026 files its GSTR-3B, due on 20 July 2026, on 10 September 2026. At ₹10 a day the 52 days come to ₹520 under each Act. The nil-return cap of ₹250 applies, so the total is ₹500. Any nil return more than 25 days late reaches the same ₹500 ceiling as one filed a year late.
Three months caught up on one day
A proprietor with ₹90 lakh turnover in FY 2025-26 misses the April, May and June 2026 returns and files all three on 15 August 2026. Section 39(10) forces him to file them in order, and each is charged separately:
| Return | Due date | Days late on 15 August 2026 | CGST fee before cap | CGST fee after ₹1,000 cap |
|---|---|---|---|---|
| April 2026 | 20 May 2026 | 87 | ₹2,175 | ₹1,000 |
| May 2026 | 20 June 2026 | 56 | ₹1,400 | ₹1,000 |
| June 2026 | 20 July 2026 | 26 | ₹650 | ₹650 |
The CGST late fee totals ₹2,650 and the SGST fee matches it, so ₹5,300 goes out in cash. If the GSTR-1 for those months is also late, a second set of fees follows on the same pattern.
GSTR-9 on time, GSTR-9C two months later
A company with ₹14 crore aggregate turnover in FY 2025-26, all from one State, must file both GSTR-9 and GSTR-9C by 31 December 2026. It files GSTR-9 on 15 January 2027 and GSTR-9C on 15 March 2027. The fee runs to 15 March, which is 74 days. At ₹50 a day under each Act that is ₹3,700, against a cap of 0.02% of ₹14 crore, or ₹28,000. The total is ₹7,400. Filing both forms on 15 January would have cost ₹1,500.
The percentage caps rarely bite for larger taxpayers. A company with ₹60 crore aggregate turnover whose GSTIN in one State has ₹25 crore of turnover pays ₹100 a day under each Act. Its CGST cap is 0.25% of ₹25 crore, or ₹6,25,000. A return 120 days late costs ₹12,000 under each Act, ₹24,000 in total, nowhere near the cap.
Why GSTR-9C keeps the annual return open
The previous example follows Circular 246/03/2025-GST dated 30 January 2025. Where GSTR-9C is required, the circular treats GSTR-9 and GSTR-9C together as the annual return. The return is complete only when both are filed. The late fee is not charged twice; it runs from the due date to the date the later of the two forms is furnished.
For FY 2017-18 to FY 2022-23, Notification 08/2025-Central Tax waived the fee that had built up between GSTR-9 and a later GSTR-9C, but only if the GSTR-9C was filed by 31 March 2025, and fees already paid were not refunded. The notification does not reach FY 2023-24 or later years, so for those years a pending GSTR-9C keeps the meter running. What goes into the reconciliation is covered in the GSTR-9 and GSTR-9C checklist.
Who does not pay a GSTR-9 late fee at all
A late fee arises only where a return is required. Notification 15/2025-Central Tax dated 17 September 2025 exempts registered persons whose aggregate turnover in a financial year is up to ₹2 crore from filing the annual return for FY 2024-25 onwards. A business in that band that does not file GSTR-9 is not in default, so there is nothing to compute.
The exemption is tested year by year. Take a business with ₹1.8 crore of turnover in FY 2025-26 and ₹2.3 crore in FY 2026-27. It need not file GSTR-9 for the first year, but it must file for FY 2026-27 by 31 December 2027. If it misses that date, the ₹25-a-day CGST rate starts running from 1 January 2028.
Paying the fee from the cash ledger
Section 49 of the CGST Act allows the electronic credit ledger to be used only for output tax. The electronic cash ledger can pay tax, interest, penalty and fees. Input tax credit cannot settle a late fee, however large the credit balance, and the portal's GSTR-3B manual says the same. Money has to be deposited by challan first; how the three ledgers interact is set out in the guide to the cash ledger, credit ledger and liability register.
The portal works out the GSTR-3B fee from the filing date and adds it to the payment table. According to its manual, the late fee shown for a month includes the fee for delay in filing the previous month's GSTR-3B. Any outstanding fee also blocks the nil-filing option: the GSTR-3B FAQs list "no outstanding interest or late fee liability" as a condition for filing a nil return.
Interest is a separate charge under section 50 on tax paid late. A return filed 45 days late with tax payable attracts both. The interest calculation, including the relief for tax paid in cash, is explained in how GST interest on late payment is calculated.
Past amnesties and the three-year filing bar
Relief beyond the standing caps has come only through notifications for a class of taxpayers, each with a fixed window. Notification 19/2021 capped the fee for unfiled GSTR-3B returns from July 2017 to April 2021 at ₹500 under the CGST Act (₹250 for nil returns) if they were filed between 1 June and 31 August 2021. Notification 07/2023 capped the old GSTR-9 fee at ₹10,000 under the CGST Act for returns up to FY 2021-22 filed between 1 April and 30 June 2023. All those windows are closed.
Waiting for another one has become riskier. From 1 October 2023, section 37(5) and section 39(11) stop a GSTR-1 or a return under section 39 from being furnished after three years from its due date. Section 39(11) lets the Government relax this for a class of taxpayers by notification, but no taxpayer can count on that. A late fee does not keep the door open. Once three years pass, the return cannot be filed at all, and the default can no longer be cured by paying the capped fee.
So for any GSTIN with pending returns, list each return with its due date, file the oldest first because section 39(10) requires it, and keep track of the date three years after each due date. If returns have been pending long enough for the registration to be suspended or cancelled, start with the steps in what suspension, cancellation and revocation of GST registration mean.
