Late GST filings cost money on two independent meters: a late fee under Section 47 (per day, but capped) and interest under Section 50 (18% a year, uncapped). Many taxpayers still budget with the old Rs. 100-200 per day figures or assume interest applies to the whole tax – both wrong since the June 2021 rationalisation and the net-cash-liability amendment. Here are the numbers that actually apply in FY 2026-27, plus a deadline rule introduced in 2025 that can permanently lock you out of filing.
Late fee rates and caps – FY 2026-27
| Return | Late fee per day | Maximum (cap) |
|---|---|---|
| GSTR-3B / GSTR-1 (regular) | Rs. 50 (25 CGST + 25 SGST) | AATO up to Rs. 1.5 Cr: Rs. 2,000; Rs. 1.5-5 Cr: Rs. 5,000; above Rs. 5 Cr: Rs. 10,000 |
| GSTR-3B / GSTR-1 (nil) | Rs. 20 (10 + 10) | Rs. 500 |
| GSTR-4 (composition annual) | Rs. 50 | Rs. 2,000 (nil: Rs. 500) |
| GSTR-7 (TDS) | Rs. 50 | Rs. 2,000; nil GSTR-7 fully waived (Notfn 23/2024) |
| GSTR-9 (FY 2022-23 onwards) | Rs. 50 / 100 / 200 by turnover | 0.04% of state turnover (up to Rs. 20 Cr AATO); 0.50% above |
| CMP-08 | No late fee | Interest only |
The caps are per return, set by Notifications 19/2021 and 20/2021 (and 07/2023 for the annual return). The fee splits equally between CGST and SGST; there is no late fee under the IGST Act.
Interest under Section 50 – only on the cash component
Interest runs at 18% per annum, day-wise, from the day after the due date to the date of payment – but only on the portion of tax paid through the electronic cash ledger. Tax settled through input tax credit carries no interest (proviso to Section 50(1), retrospective from 1 July 2017). ITC wrongly availed and utilised also attracts 18%.
The 3-year filing bar – the deadline that cannot be bought back
Five rules practitioners apply daily
- Late fee is cash-only – it cannot be set off against ITC, and the portal will not accept the next GSTR-3B until paid.
- GSTR-1 late fee is real even though the portal does not auto-collect it with GSTR-1 – it can be demanded later.
- Interest has no cap – on long delays it quickly exceeds the late fee.
- Deducted-but-not-deposited situations are treated more harshly than mere non-payment – pay deducted amounts first.
- Annual return delays where GSTR-9C is also required keep the Section 47 meter running until the complete annual return (including 9C) is furnished.
Compute your exact late fee and interest
Pick the return, enter the dates and cash liability – turnover caps, nil rates and the GSTR-9 percentage cap are built in.
Open GST Late Fee & Interest CalculatorFrequently Asked Questions
I filed a nil GSTR-3B six months late – what do I owe?
Rs. 20 per day capped at Rs. 500 – so Rs. 500 in total, paid in cash. No interest, since there was no tax.
Is interest calculated automatically by the portal?
The portal auto-computes late fee and shows system-computed interest in GSTR-3B (editable). You remain responsible for the correct figure – underpaid interest can be demanded with further interest.
Can late fees be waived?
Only by notification – the government has periodically run amnesty schemes for past periods. There is no officer discretion to waive Section 47 fees for routine delays.
Does the 3-year bar apply to GSTR-9 too?
Yes – it covers returns under Sections 37, 39, 44 and 52 (GSTR-1, 3B/4/5/6/7, annual return and TCS statements). Each return’s three-year clock runs from its own due date.