Every GST late fee in one place: GSTR-1, GSTR-3B, GSTR-9 (FY 2025-26)
GST late fees are rarely a large surprise on one return. They become expensive when a finance team treats filing as one monthly task, misses the return, and then discovers that the fee, interest, cash payment and customer-facing data problem are all separate consequences. For FY
Harun Raaj
Chartered Accountant · Harun Raaj & Associates
GST late fees are rarely a large surprise on one return. They become expensive when a finance team treats filing as one monthly task, misses the return, and then discovers that the fee, interest, cash payment and customer-facing data problem are all separate consequences.
For FY 2025-26, the practical way to think about the three common GST returns is simple: GSTR-1 is the outward-supplies statement, GSTR-3B is the summary return with tax payment, and GSTR-9 is the annual return. Section 47 of the CGST Act supplies the late-fee framework. The due-date JSON gives the FY 2025-26 filing dates. Notification No. 84/2020 explains the different rhythm for QRMP taxpayers.
This is a working guide, not a substitute for the current GSTN computation. The cited GST references themselves flag the caps and exemption position for verification.
The short answer
The daily amount is not the same thing as the maximum amount. For GSTR-1 and GSTR-3B, the entries say the cap is notification-based. For GSTR-9, the entry states the 0.25% turnover cap. So a spreadsheet that multiplies days by a rate without applying the correct cap is not a liability calculation; it is only a first estimate.
GSTR-1: the return that starts the customer-data chain
For monthly filers, the FY 2025-26 due-date entry says GSTR-1 is due on the 11th of the following month. The same entry says QRMP quarterly filers file on the 13th of the month after the quarter ends. Notification No. 84/2020 describes the quarterly cycle as Q1 by 13 July, Q2 by 13 October, Q3 by 13 January and Q4 by 13 April.
Section 47's base amounts are ₹50 per day for a taxable-supply return or ₹20 per day for a nil return. The penalty entry describes the split as ₹25 CGST plus ₹25 SGST for the taxable rate, and ₹10 plus ₹10 for the nil rate. Its examples are deliberately mechanical:
- A nil GSTR-1 filed 20 days late produces ₹20 × 20 = ₹400, subject to the notification cap.
- A taxable GSTR-1 filed 15 days late produces ₹50 × 15 = ₹750, subject to the notification cap.
The operational point is more important than the arithmetic. GSTR-1 carries outward-supply data that customers and the rest of your GST close process depend on. A late fee is visible, but a late statement can also create reconciliation work. Build the filing date into the invoice-close calendar, then reserve a separate check for amendments and missing invoices.
⚠ Verify: Late-fee caps under GSTR-1 change through CBIC notifications and budget amendments. Verify the current maximum for your annual aggregate turnover slab on the GSTN portal before computing liability.
GSTR-3B: late fee plus possible interest
For FY 2025-26, the due-date entry gives the monthly structure as the 20th of the following month. It notes that QRMP filers use the 22nd or 24th after quarter end. The penalty entry also distinguishes the turnover and filing categories: monthly taxpayers above ₹5 crore are shown with the 20th structure, while QRMP quarterly taxpayers at or below ₹5 crore are shown with the 22nd/24th structure.
Section 47 gives a base late fee of ₹50 per day for a return with liability and ₹20 per day for a nil return. The Section 47 examples are:
- Tax-payable return, 25 days late: ₹50 × 25 = ₹1,250, shown as ₹625 CGST and ₹625 SGST.
- Nil return, 40 days late: ₹20 × 40 = ₹800, shown as ₹400 CGST and ₹400 SGST.
But GSTR-3B is different from GSTR-1 because it is also the tax-payment return. Section 50 CGST provides 18% per annum simple interest on the net cash liability, calculated from the day after the due date until payment. The worked example for ₹50,000 paid 30 days late is ₹50,000 × 18% ÷ 365 × 30 = ₹739.
That means the GSTR-3B close should carry two separate questions: how many days late was the return, and how much net cash tax remained unpaid for how long? Do not hide interest inside the late-fee line. Section 50 CGST provides that interest is on net cash liability after eligible ITC, but it also asks the GST practitioner to confirm cases where ITC eligibility is disputed.
⚠ Verify: The current GSTR-3B maximum late fee varies by taxpayer category because CBIC has periodically waived or capped it. Check the GSTN portal and the latest applicable notification for FY 2025-26.
⚠ Verify: For section 50, confirm the net-cash base where ITC eligibility is disputed. Under s.50 CGST the 18% rate applies to net cash liability, not the full tax, but the case facts still matter.
GSTR-9: the annual return with a turnover cap
The FY 2025-26 due-date entry says GSTR-9 is due on 31 December 2026. Its late-fee entry states ₹200 per day, with a maximum of 0.25% of annual aggregate turnover in the state. The penalty entry expresses the calculation as the lesser of the accumulated daily amount and the cap.
The cited GSTR-9 reference examples make the cap concrete:
- State turnover ₹50 lakh, 30 days late: daily fee ₹6,000; 0.25% cap ₹12,500; fee remains ₹6,000.
- State turnover ₹2 crore, 90 days late: daily fee ₹18,000; 0.25% cap ₹50,000; fee remains ₹18,000.
The date basis in the penalty data is days from 31 December to the actual filing date. For the FY 2025-26 return, start with 31 December 2026 as the stated due date and then calculate the delay under the portal's filing treatment.
There is an important eligibility caveat. The FY 2025-26 GSTR-9 due-date reference says the exemption threshold for small taxpayers has changed through notifications, and the cited GSTR-9 reference explicitly requires verification of whether the company needs GSTR-9. Do not decide that question from a remembered threshold. Check the current GSTN position before computing any late fee.
⚠ Verify: Confirm the GSTR-9 exemption threshold for FY 2025-26 on the GSTN portal. The source data records the prior threshold history but does not authorise treating it as the current rule.
QRMP changes the calendar, not the discipline
Notification No. 84/2020 permits taxpayers with annual aggregate turnover of ₹5 crore or less in the preceding financial year to opt for QRMP. The notification says GSTR-1 and GSTR-3B are filed quarterly, while tax for the first two months is paid monthly through PMT-06.
The monthly PMT-06 payment is due by the 25th of the following month for Month 1 and Month 2 of the quarter. The notification records two payment methods: the Fixed Sum Method, stated as 35% of the previous quarter's cash liability, and the Self-Assessment Method, based on actual monthly liability. QRMP filers can also use IFF for B2B invoices for Month 1 and Month 2 by the 13th of the following month.
For a founder, the risk is calendar confusion. A quarterly return does not mean quarterly attention. There are still monthly payments, optional invoice furnishing, a quarterly GSTR-1, a quarterly GSTR-3B, and a year-end GSTR-9 decision. Put each on a separate control line.
⚠ Verify: If turnover crossed ₹5 crore during the year, confirm the exact QRMP exit cut-off and transition procedure on the GSTN portal before changing the filing calendar.
A practical late-fee control for FY 2025-26
Use one register with one row per return and these columns: GSTIN, tax period, return, filing category, statutory due date, actual filing date, days late, taxable or nil status, daily rate, cap, late fee, net cash liability, interest days, and reviewer sign-off.
At month-end, finance should record whether the return is ready, not merely whether someone has opened the portal. At filing, save the acknowledgement and the system-computed amount. At the next close, reconcile the booked liability to the portal. For QRMP, add PMT-06 and IFF as distinct rows so the quarter does not conceal a missed monthly control.
If a return is late, calculate the fee and interest separately, apply the correct cap, record the applicable statutory section, and flag any citation-file verification item. That makes the CA review focused: category, date, base, cap, and payment evidence.
Statutory basis
- Section 47 CGST — GSTR-1
- Section 47 CGST — GSTR-3B
- Section 47 CGST — GSTR-9
- Section 50 CGST — interest on late payment
- GSTR-1 monthly due date
- GSTR-3B monthly due date
- GSTR-9 due date
- Notification No. 84/2020 — QRMP
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See Also
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Statute-cited, section-by-section guides covering the same ground this article does.
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