GSTR-9 and GSTR-9C

What Is GSTR-9 and GSTR-9C?

GSTR-9 is the annual return a regular GST-registered taxpayer in India files, summarising a full financial year's outward supplies, inward supplies, input tax credit, and tax paid across the monthly or quarterly returns already filed. Taxpayers whose aggregate turnover is up to ₹2 crore are exempt from filing it altogether. GSTR-9C is a separate self-certified reconciliation statement — filed only by taxpayers whose aggregate turnover in that financial year exceeds ₹5 crore — that ties the figures reported in GSTR-9 back to the taxpayer's audited annual financial statements. Both are filed together, electronically, on or before 31 December following the end of the financial year.

For a foreign-owned Indian subsidiary or branch, the sequence is a two-step ladder. Below ₹2 crore of aggregate turnover, no annual return is due at all. Between ₹2 crore and ₹5 crore, GSTR-9 alone. Above ₹5 crore, GSTR-9 plus GSTR-9C — an annual reconciliation exercise the finance team, not a Chartered Accountant, certifies itself.

Legal Basis

Section 44 of the CGST Act, 2017 — Annual Return

Section 44(1) of the Central Goods and Services Tax Act, 2017 requires every registered person — other than an Input Service Distributor, a person paying tax under section 51 (TDS) or section 52 (TCS, e-commerce operators), a casual taxable person, and a non-resident taxable person — to furnish an annual return for every financial year, "which may include a self-certified reconciliation statement, reconciling the value of supplies declared in the return furnished for the financial year, with the audited annual financial statement," within the time and form prescribed. The Commissioner may, on the GST Council's recommendation, exempt any class of registered persons from filing the annual return by notification, and the section does not apply to government departments and local authorities whose accounts are audited by the Comptroller and Auditor-General.

This is the current text of section 44(1), substituted by section 111 of the Finance Act, 2021 and brought into force from 1 August 2021 via Notification No. 29/2021-Central Tax. The phrase "self-certified reconciliation statement" is doing the real work here. Before this amendment, the old section 44(2) required a taxpayer whose accounts had to be audited under section 35(5) to file the audited annual accounts and a reconciliation statement alongside the annual return, and the old Rule 80(3) required that statement to be "duly certified" — in practice, by a Chartered Accountant or Cost Accountant. Both the audit reference and the certification requirement are gone.

Section 44(2), inserted by section 144 of the Finance Act, 2023 with effect from 1 October 2023 (Notification No. 28/2023-Central Tax), adds a hard stop: a registered person cannot furnish an annual return for a financial year after three years from its due date, unless the Government notifies an extension for a specified class of taxpayers.

The ₹2 Crore Exemption From GSTR-9

The first proviso to section 44(1) lets the Commissioner exempt a class of registered persons from the annual return by notification, and that power has been exercised every year since FY 2018-19. The exemption is no longer year-by-year. Notification No. 15/2025 – Central Tax, dated 17 September 2025, exempts, “in respect of filing of annual return for the financial year 2024-25 onwards … the registered person whose aggregate turnover in any financial year is up to two crore rupees, from filing annual return that said financial year.” It is open-ended: unlike the annual notifications that preceded it (Notification No. 14/2024 – Central Tax for FY 2023-24, No. 32/2023 for FY 2022-23, No. 10/2022 for FY 2021-22, No. 31/2021 for FY 2020-21), it does not have to be renewed each year, and it stands unamended.

The exemption is optional in practice — a taxpayer below ₹2 crore may still file GSTR-9 voluntarily — and it covers GSTR-9 only. It says nothing about GSTR-9C, which is set by Rule 80(3) and in any event only starts at ₹5 crore.

Rule 80 of the CGST Rules, 2017 — Forms, Threshold and Due Date

Rule 80 translates section 44 into the actual forms and numbers. Rule 80(1) requires every person covered by section 44 to file the annual return in FORM GSTR-9, electronically through the common portal, on or before 31 December following the end of the financial year (a composition taxpayer under section 10 files FORM GSTR-9A instead). Rule 80(3) — substituted by Notification No. 30/2021-Central Tax dated 30 July 2021, the same amendment round that rewrote section 44(1) — requires every registered person (other than the section 44 exclusions) whose aggregate turnover during the financial year exceeds ₹5 crore to also furnish a self-certified reconciliation statement in FORM GSTR-9C, filed along with GSTR-9 by the same 31 December due date.

Before the 30 July 2021 substitution, Rule 80(3) set the GSTR-9C threshold at turnover exceeding ₹2 crore (raised to ₹5 crore for FY 2018-19 and FY 2019-20 by a subsequent proviso), and required the taxpayer to "get his accounts audited as specified under sub-section (5) of section 35" and furnish "a copy of audited annual accounts and a reconciliation statement, duly certified" — the CA/CMA-certified audit report that GSTR-9C originally was. The current rule drops both the mandatory audit reference and the certification requirement, leaving a single ₹5 crore threshold and a statement the taxpayer certifies itself.

Who Actually Files What

• FORM GSTR-9 — every regular registered person, for every financial year, unless they fall into one of the section 44(1) exclusions (Input Service Distributor, TDS deductor under section 51, e-commerce operator/TCS collector under section 52, casual taxable person, non-resident taxable person) or their aggregate turnover for the year is up to ₹2 crore, in which case Notification No. 15/2025 – Central Tax exempts them.
• FORM GSTR-9A — composition taxpayers under section 10, in place of GSTR-9 (Rule 80(1), proviso).
• FORM GSTR-9C — only registered persons (outside the section 44 exclusions) whose aggregate turnover for the financial year exceeds ₹5 crore, filed as a self-certified reconciliation statement alongside GSTR-9.

A GST-registered Indian subsidiary of a foreign parent with turnover of, say, ₹3 crore in a financial year files only GSTR-9. At ₹1.5 crore it would file nothing. Once that subsidiary's turnover crosses ₹5 crore, GSTR-9C becomes mandatory alongside GSTR-9 — with no CA or CMA sign-off required, but with the finance team on the hook for the accuracy of the reconciliation.

What GSTR-9C Actually Reconciles

GSTR-9C compares the turnover, tax liability, and input tax credit figures reported across the year's GSTR-1 and GSTR-3B returns (as consolidated in GSTR-9) against the audited financial statements for the same financial year — the profit and loss account and balance sheet prepared under the Companies Act, 2013 or other applicable accounting framework. Because most companies above the ₹5 crore GST turnover threshold are also within reach of a statutory audit under company law, the underlying audited numbers GSTR-9C reconciles against already exist for other reasons — GSTR-9C simply requires the taxpayer to reconcile GST-return turnover to that audited turnover and explain any difference (unbilled revenue, deemed supplies, advances, credit notes, and similar timing or classification differences) rather than to commission a fresh audit of its own.

Due Date and the Three-Year Time Bar

Both GSTR-9 and, where applicable, GSTR-9C are due on 31 December following the end of the relevant financial year (Rule 80(1) and 80(3)) — for financial year 2025-26, that is 31 December 2026. Rule 80(1A) and 80(3A) record a one-off extension granted for financial year 2020-21, when both filings were pushed to 28 February 2022; no comparable blanket extension applies to later years unless separately notified. Under section 44(2), a taxpayer cannot file an annual return for a given financial year more than three years after that year's original due date, except where the Government notifies a specific extension for a class of taxpayers.

Late Fee for Missing the Deadline

Section 47(2) of the CGST Act fixes the statutory late fee for a delayed annual return: ₹100 for every day of default, capped at one-quarter of one per cent (0.25%) of the taxpayer's turnover in the State or Union Territory — a separate and distinct late fee from section 47(1), which caps delayed monthly and quarterly returns at ₹5,000. Both figures are the CGST amount; an equal late fee runs under the corresponding State or Union Territory GST Act, so the cash cost is double the figure in the section.

For most businesses the statutory rate is not what is actually charged. Notification No. 07/2023 – Central Tax, dated 31 March 2023, waives the excess over a reduced amount for the annual return “for the financial year 2022-23 onwards”:

• Aggregate turnover up to ₹5 crore in the relevant financial year — ₹25 per day, capped at 0.02% of turnover in the State or Union Territory.
• Aggregate turnover above ₹5 crore and up to ₹20 crore — ₹50 per day, capped at 0.02% of turnover in the State or Union Territory.
• Aggregate turnover above ₹20 crore — no reduction; the full section 47(2) rate of ₹100 per day, capped at 0.25% of turnover, applies.

Again these are CGST figures with an equal SGST or UTGST amount alongside. The reduction is standing, not year-specific, so it applies to FY 2022-23 and every year after it unless CBIC amends the notification.

Why This Matters for a Foreign Company or Investor

Two features of the current regime matter disproportionately to a foreign parent setting up in India:

• No CA/CMA certification is required for GSTR-9C anymore. This lowers the compliance cost of crossing the ₹5 crore turnover mark, but it also shifts the reconciliation risk onto the company itself — a foreign parent that assumed an external auditor would catch reconciliation errors, as under the pre-August-2021 regime, now needs its own finance team or outsourced GST-compliance provider to get it right.
• The turnover threshold is India-wide by PAN, not per GSTIN. A company with multiple GST registrations across states aggregates turnover across all of them to test the ₹5 crore GSTR-9C threshold — a group with several smaller state-level GSTINs can still be pulled into GSTR-9C once its combined turnover crosses the line.
• The three-year time bar under section 44(2) means a foreign-invested entity that has fallen behind on annual returns for a closed financial year cannot simply catch up whenever convenient — filing must happen within three years of the original due date unless a specific government notification says otherwise.

Practical Example

Meridian India Pvt Ltd, a wholly-owned subsidiary of a Singapore-based technology company, has a single GST registration in Karnataka. In financial year 2025-26 its aggregate turnover is ₹6.2 crore. Because that exceeds the ₹5 crore threshold in Rule 80(3), Meridian India must file both FORM GSTR-9 (summarising its outward supplies, ITC availed, and tax paid across the year's GSTR-1 and GSTR-3B filings) and FORM GSTR-9C (reconciling that GSTR-9 turnover against its audited profit and loss account for FY 2025-26) by 31 December 2026. No Chartered Accountant certification is required on the GSTR-9C — Meridian India's own authorised signatory certifies it. If the company had reported turnover of ₹4.5 crore instead, it would file only GSTR-9, with no GSTR-9C obligation at all.

Common Mistakes

• Assuming GSTR-9C still needs a CA or CMA sign-off. That requirement was removed with effect from 1 August 2021; GSTR-9C is now self-certified by the taxpayer.
• Testing the ₹5 crore threshold per GSTIN instead of on a PAN-wide aggregate turnover basis, understating whether GSTR-9C applies to a multi-state operation.
• Confusing the section 47(1) late fee (capped at ₹5,000, for routine periodic returns) with the section 47(2) late fee for the annual return, which is capped instead at a percentage of turnover and can be materially larger for a sizeable business.
• Quoting the bare section 47(2) rate without applying Notification No. 07/2023 – Central Tax, which cuts the annual-return late fee to ₹25 or ₹50 a day, capped at 0.02% of turnover, for anyone under ₹20 crore.
• Treating the annual return as optional once the periodic GSTR-1 and GSTR-3B returns are up to date. Above ₹2 crore of aggregate turnover, GSTR-9 is a separate, additional filing obligation under section 44, not a summary generated automatically from the monthly filings.

Key Takeaways

• GSTR-9 (the annual return) is filed under section 44 of the CGST Act, 2017 and Rule 80(1) of the CGST Rules, due 31 December following the end of the financial year.
• Registered persons whose aggregate turnover for the year is up to ₹2 crore are exempt from GSTR-9 for FY 2024-25 onwards, under Notification No. 15/2025 – Central Tax dated 17 September 2025.
• GSTR-9C (the reconciliation statement) applies only once aggregate turnover for the financial year exceeds ₹5 crore (Rule 80(3)), filed alongside GSTR-9 by the same date.
• Mandatory CA/CMA certification of GSTR-9C was removed with effect from 1 August 2021; the statement is now self-certified by the taxpayer.
• Section 44(2) bars filing an annual return more than three years after its original due date, absent a specific government notification.
• The statutory late fee for a delayed annual return, under section 47(2), is ₹100 per day capped at 0.25% of turnover in the State or Union Territory, but Notification No. 07/2023 – Central Tax reduces it to ₹25 or ₹50 per day, capped at 0.02% of turnover, for taxpayers up to ₹20 crore.

Frequently Asked Questions

Is every GST-registered company required to file GSTR-9?

No. Notification No. 15/2025 – Central Tax, dated 17 September 2025, exempts a registered person whose aggregate turnover in a financial year is up to ₹2 crore from filing the annual return, for FY 2024-25 onwards. Above that, GSTR-9 is due unless the taxpayer falls into one of the section 44(1) exclusions.

Does every GST-registered company have to file GSTR-9C?

No. GSTR-9C under Rule 80(3) of the CGST Rules applies only to a registered person whose aggregate turnover for the financial year exceeds ₹5 crore. A company below that threshold files only GSTR-9, the annual return, and has no GSTR-9C obligation for that year.

Is a Chartered Accountant still required to certify GSTR-9C?

No. Since Rule 80(3) was substituted with effect from 1 August 2021 (Notification No. 30/2021-Central Tax), GSTR-9C is a self-certified reconciliation statement filed by the taxpayer itself. Before that date, the rule required audited accounts and a reconciliation statement duly certified by a Chartered Accountant or Cost Accountant.

What is the due date for GSTR-9 and GSTR-9C?

Both are due on or before 31 December following the end of the relevant financial year, under Rule 80(1) and Rule 80(3) of the CGST Rules. For financial year 2025-26, the due date is 31 December 2026, unless CBIC notifies a specific extension.

What is the penalty for filing GSTR-9 late?

Section 47(2) of the CGST Act sets the late fee at ₹100 for every day of default, subject to a maximum of 0.25% of turnover in the State or Union Territory concerned, with an equal amount under the State or Union Territory GST Act. Notification No. 07/2023 – Central Tax reduces it from FY 2022-23 onwards to ₹25 per day (capped at 0.02% of turnover) up to ₹5 crore turnover and ₹50 per day (same cap) between ₹5 crore and ₹20 crore. Above ₹20 crore the full statutory rate applies.

Can a company file GSTR-9 for a financial year that closed several years ago?

Only within limits. Section 44(2) of the CGST Act, inserted with effect from 1 October 2023, bars furnishing an annual return more than three years after its original due date, unless the Government specifically notifies an extension for a class of registered persons.

See also: Goods and Services Tax (GST), GST Registration, and Statutory Audit.

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