GSTR-9 and GSTR-9C for FY 2025-26: Thresholds, 31 December 2026 Due Date and the Two-Rate Year

Table of Contents

1. Who must file, who may skip, and who is excluded
2. Due date, late fee and the three-year bar
3. The two-rate year: reporting FY 2025-26 across 21/22 September 2025
4. Table by table: what to reconcile and against what
5. GSTR-9C: the self-certified reconciliation
6. Nine errors we see in annual returns — and what they cost
7. A working plan from now to 31 December
8. Frequently asked questions

1. Who must file, who may skip, and who is excluded

Section 44(1) requires every registered person, other than the excluded categories, to furnish an annual return for each financial year. The thresholds for FY 2025-26 are:

Excluded regardless of turnover (Section 44(1) and Rule 80): Input Service Distributors, persons deducting tax under Section 51, e-commerce operators collecting tax under Section 52, casual taxable persons and non-resident taxable persons. Composition taxpayers file GSTR-9A, not GSTR-9. Government departments whose accounts are audited by the CAG are outside Section 44 as well.

Two practical points. First, "aggregate turnover" is the PAN-wide figure defined in Section 2(6) — taxable, exempt, export and inter-State supplies of all registrations added together — so a group with a ₹1.8 crore Chennai GSTIN and a ₹60 lakh Bangalore GSTIN is above ₹2 crore and files GSTR-9 for both. Second, the exemption is from filing, not from the law: a taxpayer under ₹2 crore who has short-paid tax or over-claimed ITC during the year gets no cover from not filing; the liability is simply pursued through DRC-01A and Section 73/74A instead of being self-corrected in Table 9 and Table 14. For a client below the threshold with any reconciliation difference, we recommend filing voluntarily and paying through DRC-03, because the Section 73 (or 74A) time limit then runs from the annual return's due date rather than from the date the officer finds it.

The exemption threshold interacts with our GST annual return service: we file for every client above ₹2 crore and, for those below it, give a written reconciliation memo so the decision not to file is a documented one.

2. Due date, late fee and the three-year bar

Due date. 31 December following the end of the financial year — 31 December 2026 for FY 2025-26 (Section 44(1) read with Rule 80(1)). GSTR-9C is filed along with or after GSTR-9, by the same date (Rule 80(3)). 31 December 2026 is a Thursday. Extensions have been granted in some past years in the last week of December; nothing has been notified for FY 2025-26, and the portal was opened unusually early this year, which usually signals that none is intended.

Late fee. Section 47(2) as rationalised by Notification No. 07/2023-Central Tax (31 March 2023), applicable from FY 2022-23:

There is no separate late fee for GSTR-9C; the general penalty under Section 125 (currently up to ₹25,000 under each Act, proposed to be reduced to ₹10,000 by the 57th GST Council) is the exposure for a 9C that is never filed.

The three-year bar. Section 44(2), inserted by the Finance Act, 2023 and in force from 1 October 2023, provides that a registered person "shall not be allowed to furnish" an annual return after the expiry of three years from its due date. The portal has enforced this since the second half of 2025. For FY 2025-26 that door closes on 31 December 2029; for FY 2022-23 it closed on 31 December 2026 — which is the same day the FY 2025-26 return is due. A taxpayer with an unfiled FY 2022-23 GSTR-9 has until the end of this year to file it at all, after which the liability can only be settled through a demand order.

3. The two-rate year: reporting FY 2025-26 across 21/22 September 2025

The 56th GST Council (3 September 2025) collapsed the 12% and 28% slabs into 5% and 18% (with a 40% rate for a short list of demerit and luxury goods), effective 22 September 2025. FY 2025-26 therefore has 175 days at the old rates and 190 days at the new ones. GSTR-9 is a rate-wise return, so nothing in it can be filled from a single annual figure.

• Tables 4 and 5 (outward supplies) are reported rate-wise. Goods that moved from 12% to 5%, or from 28% to 18%, appear on two lines each: supplies up to 21 September at the old rate and from 22 September at the new. Run the sales register in two date ranges and add them; do not apply one rate to the year.
• Time of supply decides the line, not the invoice date. Under Section 12 (goods) and Section 13 (services), where an invoice was issued or payment received before 22 September for a supply made after it (or the reverse), Section 14 fixes the applicable rate. Advances received before the change for services rendered after it are the usual trap.
• Credit notes issued after 22 September for pre-change supplies (Section 34) carry the rate of the original invoice. They reduce the old-rate line in Table 4 or 5, not the new-rate line, and they are reported net in the same table in which the original supply appears, with the annual-aggregate figure in Table 4I/4J.
• Table 17 (HSN-wise summary of outward supplies) — mandatory since FY 2021-22 at 6-digit HSN for turnover above ₹5 crore and 4-digit for B2B supplies below — needs one row per HSN per rate, so every re-rated product has two rows. The portal validates Table 17 against Tables 4 and 5 at the rate level.
• Table 9 (tax payable) is computed from the rate-wise taxable values; a mismatch between the sum of Tables 4 and 5 at each rate and the tax shown in Table 9 is the first thing a Section 61 scrutiny notice (ASMT-10) picks up.
• ITC is unaffected by the rate change on your purchases only in amount — you claim what the supplier charged — but the inverted-duty position of many businesses flipped on 22 September. A trader buying at 18% and selling at 5% from that date has an accumulated-credit refund claim under Section 54(3) that did not exist before; the annual return is where the accumulation becomes visible. See our note on the 57th GST Council's refund changes, which widen "Net ITC" for inverted-duty refunds from 1 November 2026.

4. Table by table: what to reconcile and against what

5. GSTR-9C: the self-certified reconciliation

Since FY 2020-21, GSTR-9C is a reconciliation statement self-certified by the taxpayer, not an audit report (Section 44 as substituted by the Finance Act, 2021; Rule 80(3)). It reconciles the audited annual financial statements with GSTR-9, GSTIN by GSTIN, which for a multi-State entity means allocating the single audited turnover across registrations in Part II, Table 5, and explaining every un-reconciled rupee in Tables 6, 8, 10 and 12.

The audited financial statements are the anchor. For a company that has used the MCA's extension of AOC-4 to 31 December 2026, the financial statements are nonetheless adopted at the AGM by 30 September 2026, so the figures for Table 5A exist; the order of work is AGM-adopted accounts → GSTR-9 → GSTR-9C, and the ITR for audit cases by 21 November 2026 sits between them (see our note on the CBDT extension and the Section 234A interest it does not stop). Table 14 of GSTR-9C — expense-wise ITC reconciliation — is where the Form 3CD clause 44 break-up of expenditure by registered/unregistered supplier is reused; prepare the two together.

Although self-certified, 9C is signed with the authorised signatory's DSC and every reconciling item becomes a statement the signatory has made under Section 44. Unexplained differences in Table 8 (reasons for un-reconciled turnover) or Table 12 (un-reconciled ITC) are what the department's scrutiny module flags for ASMT-10. We prepare the 9C working papers to the standard we would for an audit under Section 65, because a Section 65 audit is where the 9C ends up if it is wrong; our GST audit practice handles both.

6. Nine errors we see in annual returns — and what they cost

1. Reverse-charge liability never paid. Import of services from a foreign parent or SaaS vendor, GTA, legal fees, directors' sitting fees. Tax with interest at 18% under Section 50(1); the ITC is available only after payment, and only within the Section 16(4) window.
2. Table 8A difference treated as "just timing". Where 8A (GSTR-2B) is lower than 8B (availed), the excess is ineligible unless it was claimed within Section 16(4) and the supplier has since reported it. Reverse with interest under Section 50(3) before 9C rather than after DRC-01A.
3. ITC on blocked items. Section 17(5): employee group insurance, motor vehicles, construction, club memberships, CSR spend (blocked by the 2023 amendment). The 57th Council has recommended allowing ITC on employee health and life insurance and on expired stock destroyed under law, but only prospectively and only once notified.
4. Rule 42/43 not trued up. Exempt supplies (interest income, sale of land, residential rent) with common inputs. The annual computation is due by the September return following the year; the difference goes to Table 7.
5. Rule 37 non-payment reversals missed. Supplier unpaid beyond 180 days from invoice; ITC to be reversed with interest and re-availed on payment.
6. Credit notes netted against the wrong rate line in the re-rated year (above).
7. Table 17 HSN rows at the wrong digit length — the portal now rejects 2-digit codes for turnover above ₹5 crore.
8. Multi-GSTIN groups filing GSTR-9 for the big registration and forgetting the small one — the threshold is PAN-level, so the ₹40 lakh branch files too.
9. Paying additional tax in Table 9 without DRC-03. Table 9's "tax payable" column can show more than "paid", but the payment itself only happens through DRC-03, and the DRC-03 reference must be quoted in Table 14.

Each of these, if found by the officer first, arrives as a DRC-01A under Section 73 or — for FY 2024-25 onward — Section 74A, with penalty of 10% of tax (minimum ₹10,000) even in the non-fraud case once the 60-day reduced-penalty window passes. Our GST notice reply team spends most of December arguing points that a good annual return would have closed in November.

7. A working plan from now to 31 December

For the monthly compliance that feeds all of this, see GST return filing; for the credit side, input tax credit advisory; and for a refresher on the form itself, our GSTR-9 guide and annual return penalties note.

8. Frequently Asked Questions (FAQs)

Is GSTR-9 compulsory for FY 2025-26 if my turnover is ₹1.9 crore?

No. Notification No. 15/2025-Central Tax dated 17 September 2025 exempts registered persons with aggregate turnover up to ₹2 crore from filing the annual return for FY 2024-25 and later years. Turnover is measured PAN-wide across all GSTINs. Filing voluntarily remains open, and is advisable where there is a known reconciliation difference to settle through DRC-03.

Who must file GSTR-9C for FY 2025-26?

Registered persons with aggregate turnover above ₹5 crore in FY 2025-26, under Rule 80(3), for each GSTIN. It is self-certified by the taxpayer — a chartered accountant's or cost accountant's certification has not been required since FY 2020-21 — but it must reconcile with the audited financial statements.

What is the last date to claim ITC of FY 2025-26?

Under Section 16(4), ITC for invoices of FY 2025-26 must be claimed in a GSTR-3B filed by 30 November 2026 — in practice the GSTR-3B for October 2026, due 20 November 2026. ITC claimed in that return is reported in Table 8C and Table 13 of GSTR-9.

How do I report sales of a product whose rate fell from 12% to 5% on 22 September 2025?

On two lines: supplies with time of supply up to 21 September 2025 at 12% and from 22 September 2025 at 5%, in Tables 4 and 5 and again in the HSN summary in Table 17. Section 14 decides the rate where the invoice, payment and supply fall on different sides of the change date. Credit notes for pre-change supplies carry 12% and reduce the 12% line.

What is the late fee for GSTR-9 filed after 31 December 2026?

Under Section 47(2) read with Notification No. 07/2023-Central Tax: ₹50 per day (CGST + SGST) for turnover up to ₹5 crore, ₹100 per day between ₹5 crore and ₹20 crore, and ₹200 per day above ₹20 crore, subject to ceilings of 0.04%, 0.04% and 0.5% of turnover in the State respectively. GSTR-9C carries no separate late fee but the general penalty under Section 125 can apply.

Can I still file GSTR-9 for FY 2022-23?

Only until 31 December 2026. Section 44(2) bars filing an annual return after three years from its due date, and the FY 2022-23 return was due on 31 December 2023. After that the liability for that year can only be determined by the officer under Section 73.

Does the MCA extension of AOC-4 to 31 December 2026 change the GSTR-9C timeline?

No. GSTR-9C reconciles to the audited financial statements, which were adopted at the AGM by 30 September 2026 regardless of when AOC-4 is filed with the Registrar. Both GSTR-9C and AOC-4 are now due on the same day, 31 December 2026; plan the GST work to finish first.

Conclusion

FY 2025-26 is the first annual return where every rate-wise table has to be built twice, and the first December in which the three-year bar under Section 44(2) closes an earlier year on the same day the current one falls due. The thresholds are unchanged — ₹2 crore for GSTR-9, ₹5 crore for GSTR-9C — and so is the lesson: the annual return is the last point at which a difference can be settled on your own terms, with interest but without the 10% penalty and without a notice on the record. Start from the 22 September split, close the Section 16(4) window on 20 November with everything found, and file in the second week of December. If you would like the reconciliation done and documented, our GST annual return service covers GSTR-9 and GSTR-9C for all GSTINs, reviewed by CA V. Viswanathan (FCA, ACS, CFE) before filing.