GSTR-9 Annual Return: Eligibility, Due Date, and Late Fees

The GSTR-9 annual return is the consolidated GST filing that every registered taxpayer must submit at the end of each financial year, pulling together all monthly or quarterly returns into one reconciled document covering outward supplies, inward supplies, input tax credit, and tax paid. For FY 2025–26, it is due on December 31, 2026. Businesses with aggregate turnover up to two crore rupees have historically been exempted by annual notification, and a handful of registration categories are excluded by statute. The return cannot be revised once filed, which makes the preparation work matter more than the submission itself.

Who Has to File and Who Doesn’t

Section 44 of the CGST Act requires every registered person to furnish an annual return, with five categories carved out directly by statute.¹ You do not need to file GSTR-9 if you are:

An Input Service Distributor.
A person deducting tax at source under Section 51.
An e-commerce operator collecting tax at source under Section 52.
A Casual Taxable Person.
A Non-Resident Taxable Person.

Composition scheme taxpayers used to file a separate Form GSTR-9A, but that requirement was dropped from FY 2019–20 onward, and composition dealers are now exempt from any annual return form.²

The Two-Crore Turnover Exemption

The Commissioner has the power under Section 44 to exempt any class of registered persons from filing, and the government has consistently used that power to exempt taxpayers whose aggregate turnover does not exceed two crore rupees.¹ For FY 2024–25, the exemption came through Notification No. 15/2025-Central Tax. A similar notification is expected for FY 2025–26, but confirm it has been issued before deciding not to file.

Filing voluntarily below the threshold is worth considering. The return acts as documented proof that your periodic filings were accurate, which helps during any later audit. If your turnover sits close to two crore, filing preemptively avoids the risk of a miscalculation pushing you into mandatory territory after the deadline has passed.

Due Date and the Three-Year Cutoff

GSTR-9 is due on December 31 of the year following the relevant financial year. For FY 2025–26 (April 2025 through March 2026), that means December 31, 2026. The government sometimes extends this date by notification, so check the CBIC portal as the deadline approaches.

Section 44(2) also bars you from filing an annual return more than three years after its due date.¹ If you miss that window entirely, the government may allow filing through a separate notification, but there is no guarantee. Letting an annual return lapse beyond this cutoff leaves a permanent gap in your compliance record.

What to Reconcile Before You Start

The annual return pulls data from your periodic filings and your books. Have the following ready before you open the portal:

GSTR-1 data covering your outward supply details, amendments, and credit or debit notes.
GSTR-3B data showing month-by-month tax paid, ITC claimed, and reversals.
GSTR-2A and GSTR-2B statements. Table 8A of GSTR-9 draws directly from GSTR-2A, and reconciling this against your books is where most of the preparation time goes.³
HSN summaries for outward and inward supplies.³
Audited financial statements for the year.
Records of any interest, late fees, or penalties already paid during the year.

The single biggest source of filing pain is a mismatch between the turnover reported in GSTR-1, the liability paid through GSTR-3B, and the figures in your audited financials. Timing differences, late credit notes, and vendor filing delays all contribute. Reconcile the three data sets against each other before touching the portal.

How the Form Is Organized

GSTR-9 is broken into tables that each capture a different slice of the year’s activity. Some tables auto-populate from your GSTR-3B, but you are responsible for verifying and editing the figures where needed.⁴

Table 4 captures outward supplies on which tax is payable, including taxable sales, exports, and supplies to SEZs.
Table 5 covers outward supplies on which tax is not payable, including exempt, nil-rated, and non-GST supplies.
Table 6 records ITC availed, split into inputs, capital goods, and input services.
Table 7 records ITC reversed and ineligible ITC.
Table 8 handles other ITC-related information, including credit as per GSTR-2A against ITC actually claimed.
Table 9 shows tax payable versus tax paid, auto-populated from GSTR-3B but editable.
Tables 17 and 18 hold HSN-wise summaries for outward and inward supplies.

Table 9 deserves particular attention. The tax payable column pulls from your GSTR-3B net liability, but you can edit it if annual reconciliation reveals a different figure. If reconciliation shows you owe more than what was paid through monthly returns, that additional liability must be discharged separately through Form DRC-03 before or along with filing.⁴

Paying a Shortfall Through DRC-03

When annual reconciliation reveals additional tax owed, the shortfall cannot be paid inside GSTR-9. Instead, you file Form GST DRC-03 as a voluntary payment intimation, selecting “Annual return” or “Reconciliation statement” as the cause of payment. The tax component can be paid from both cash and credit ledgers, but any interest or penalty must come from the cash ledger only.⁵ A saved DRC-03 draft expires after 15 days if not submitted.

When a Nil Return Is Allowed

If your registration was active during the year but you had no business activity at all, you can file a nil GSTR-9. The portal offers a simplified flow, and most tables are skipped.⁴ A nil return is only valid if you made no outward supplies, received no inward supplies, claimed no ITC, claimed no refund, have no other liability to report, and received no demand order during the year. Fail any one of these, and you must file a regular GSTR-9.

Submission and the No-Revision Rule

Once all tables are complete, you click “Compute Liabilities” on the portal to calculate outstanding amounts, then move to the submission screen for a final review.⁴ You verify using either a Digital Signature Certificate or an Electronic Verification Code sent to your registered mobile and email. Successful verification generates an Application Reference Number.

The critical point: GSTR-9 cannot be revised after submission. Unlike periodic returns, where you can correct an error next month, the annual return is final. If you discover a mistake after filing, your only recourse is to address it in the next financial year’s return (for errors within the rectification window under Section 39(9)) or through other available mechanisms. That finality is why reconciliation before submission matters more here than in any monthly return.

GSTR-9C for Turnover Above Five Crore

Taxpayers with aggregate turnover exceeding five crore rupees during a financial year must also file GSTR-9C, a reconciliation statement bridging GSTR-9 and the audited annual financial statements. The threshold was set by CBIC Notification No. 30/2021. Since FY 2020–21, the requirement for a Chartered Accountant or Cost Accountant to certify GSTR-9C has been removed, and taxpayers now self-certify using DSC or Aadhaar-based e-sign.

The annual return under Section 44 is considered complete only when both GSTR-9 and GSTR-9C, where applicable, have been furnished. If you are required to file GSTR-9C but only submit GSTR-9, the late fee clock keeps running until the reconciliation statement is also filed.⁶ The fee is not charged separately for each form; it is calculated once, based on the delay in completing the entire annual return, and the completion date is whichever form you file last.

Late Fees

Section 47(2) of the CGST Act sets the statutory late fee at one hundred rupees per day under the central act, with an identical amount under the respective state or union territory act, for a combined statutory rate of two hundred rupees per day.⁷ The statutory maximum is 0.25% of turnover in the state or union territory per act, or 0.50% combined.

In practice, Notification No. 07/2023-Central Tax has reduced the applicable rates for most taxpayers from FY 2022–23 onward:

Turnover up to five crore rupees: Rs 25 per day under CGST plus Rs 25 under SGST/UTGST, totaling Rs 50 per day, capped at 0.04% of turnover in the state or union territory (0.04% combined).
Turnover above five crore and up to twenty crore rupees: Rs 50 per day under CGST plus Rs 50 under SGST/UTGST, totaling Rs 100 per day, with the same 0.04% cap.
Turnover above twenty crore rupees: the full statutory rate of Rs 200 per day, with the 0.50% combined cap.

To put this in concrete terms: a business with Rs 3 crore turnover filing 30 days late owes Rs 1,500 (Rs 50 × 30 days), capped at Rs 12,000 (0.04% of Rs 3 crore). A business with Rs 25 crore turnover filing 30 days late owes Rs 6,000 (Rs 200 × 30 days), capped at Rs 1,25,000 (0.50% of Rs 25 crore). The jump in cap rate above twenty crore is where the penalty starts to bite.

What Happens If You Keep Ignoring the Return

Late fees are the immediate cost, but not the only one. Tax authorities can issue a notice under Section 46 requiring you to file within a specified period. If you still fail to comply, the proper officer can proceed to a best judgment assessment under Section 62, estimating your tax liability and issuing a demand for tax, interest, and penalty based on available information. The officer has up to five years from the annual return’s due date to pass such an order.

You get a window to fix this. Filing the required return within 60 days of the assessment order causes it to be deemed withdrawn. A further 60-day extension (120 days total) is available, though the additional period attracts a late fee of Rs 100 per day. After 120 days, the assessment order stands, and you face a formal demand with far less room to negotiate.

Common Mistakes to Catch Before Filing

Most GSTR-9 errors stem from inadequate reconciliation rather than misunderstanding the form. Since the return cannot be revised, each error becomes permanent once you submit.

Turnover mismatches between GSTR-1, GSTR-3B, and audited financials. Timing differences and late amendments are usually the cause. Reconcile all three before filing.
ITC overclaim, where credit claimed in GSTR-3B exceeds what appears in GSTR-2B because suppliers filed late or filed incorrectly. The annual return is where this becomes visible to the department.
Reverse charge misreporting, where expenses booked in the financials carry reverse charge liability that was never paid through GSTR-3B, yet the corresponding ITC was still claimed. Report reverse charge in the year of payment, not booking.
Missing exempt and nil-rated supplies. Zero-rated exports, exempt supplies, and branch transfers often appear in the financial statements but get omitted from GST returns. Table 5 is where they belong.
ITC classification errors, when splitting credit across inputs, input services, and capital goods trips up taxpayers who did not maintain the distinction in monthly filings.

The time to catch these is during preparation. Once the return is filed, they stay in the record.

1
Central Board of Indirect Taxes and Customs. CGST Act 2017 – Section 44 – Annual Return
2
Goods and Services Tax Portal. FAQs – About Form GSTR-9A
3
Goods and Services Tax Portal. FAQs on Form GSTR-9
4
Goods and Services Tax Portal. Manual – GSTR-9 Annual Return
5
Goods and Services Tax. Manual – GST Form DRC-03
6
Central Board of Indirect Taxes and Customs. Circular No. 246/03/2025-GST – Clarification on Applicability of Late Fee for Delay in Furnishing of Form GSTR-9C
7
Central Board of Indirect Taxes and Customs. CGST Act 2017 – Section 47 – Levy of Late Fee