GST Annual Return Late Fee: GSTR-9 Rates, Caps & GSTR-9C | 2026

GST annual return late fee applies when the annual return required under Section 44 is furnished after the applicable due date. For GSTR-9, Section 47(2) provides the statutory late-fee framework, while Notification No. 07/2023-Central Tax rationalises the rate and cap for specified turnover bands from FY 2022-23 onward. Where GSTR-9C is required, CBIC Circular No. 246/03/2025-GST clarifies that the late-fee clock can continue until the complete annual return—GSTR-9 plus GSTR-9C—is furnished.

This guide explains the current framework for delayed GSTR-9 filing, the reduced late-fee structure applicable from FY 2022-23 onwards for specified turnover bands, the position for larger taxpayers, and the practical controls businesses should complete before filing an overdue annual return.

GST annual return late fee: freshness check — 3 September 2026

Current-source check: Section 47(2) of the CGST Act continues to govern late fee for delayed annual returns. CBIC Circular No. 246/03/2025-GST dated 30 January 2025 continues to clarify that, where GSTR-9C is required, the annual return is complete only when both GSTR-9 and GSTR-9C are furnished. The reduced turnover-band rates discussed below arise from Notification No. 07/2023-Central Tax; any later waiver, extension or notification should be checked before filing.

What is Form GSTR-9?

Form GSTR-9 is the annual return for regular GST taxpayers. The GST portal describes it as a once-a-year return containing details of outward supplies, inward supplies, input tax credit, refunds and demands for the relevant financial year. Once filed, the return cannot be revised on the portal, which makes pre-filing reconciliation particularly important.

GST annual return late fee: Section 47 and the current rate framework

Section 47(2) of the Central Goods and Services Tax Act, 2017 provides a specific late-fee rule for failure to furnish the annual return required under Section 44 by the due date. Under the statutory ceiling, the Central Tax component is ₹100 per day, subject to a maximum of 0.25% of turnover in the State or Union territory. A corresponding State/UT GST component generally applies separately.

However, the Government used its waiver power under Section 128 to rationalise the amount for specified taxpayers from FY 2022-23 onwards through Notification No. 07/2023-Central Tax dated 31 March 2023.

GSTR-9 late fee from FY 2022-23 onwards

For registered persons with aggregate turnover up to ₹5 crore in the relevant financial year, Notification No. 07/2023-Central Tax limits the Central Tax late fee to ₹25 per day, subject to a maximum of 0.02% of turnover in the State or Union territory. With the corresponding State/UT component, the commonly understood combined exposure is ₹50 per day, subject to the corresponding combined cap.

For registered persons with aggregate turnover above ₹5 crore and up to ₹20 crore, the notification limits the Central Tax component to ₹50 per day, subject to a maximum of 0.02% of turnover in the State or Union territory. With the corresponding State/UT component, the commonly understood combined exposure is ₹100 per day, subject to the corresponding combined cap.

For taxpayers above the turnover bands covered by the notification, the reduced notification-based slab does not apply merely because the return is GSTR-9. The statutory Section 47(2) framework therefore requires separate review.

Simple examples of the late-fee cap

Example 1: Assume a registered person has turnover of ₹4 crore in a State and files GSTR-9 late. The Central Tax cap under Notification No. 07/2023 is 0.02% of ₹4 crore, i.e. ₹8,000. The daily Central Tax rate is ₹25, so the Central component stops increasing once the lower applicable cap is reached. The corresponding State/UT component must be considered separately.

Example 2: Assume turnover of ₹12 crore in a State. The Central Tax cap at 0.02% works out to ₹24,000, with the Central daily amount at ₹50. Again, the State/UT GST component is separate.

Is GSTR-9 late fee the same as GSTR-3B or GSTR-1 late fee?

No. GSTR-9 is governed by the annual-return late-fee provision in Section 47(2). GSTR-1 and GSTR-3B involve different statutory and notification frameworks. Tax teams should therefore avoid applying the late-fee cap of one return type to another.

Related PGT guidance: GSTR-9C late fee for FY 2025-26, GSTR-9 due date for FY 2025-26, and GST late-fee waiver under Section 128.

What happens on the GST portal when GSTR-9 is filed late?

The GST portal’s official GSTR-9 filing manual states that after the taxpayer completes the annual-return tables and clicks “Compute Liabilities”, the portal processes the data and computes late fee where the annual return is delayed beyond the due date. The late-fee tile must then be addressed before filing. The portal also states that the electronic cash ledger and liability register are updated when the late-fee liability is set off.

Can additional tax liability be paid through GSTR-9 itself?

GSTR-9 is primarily an annual return and reconciliation document. The GST portal manual directs taxpayers to Form GST DRC-03 for additional liabilities disclosed while preparing the annual return. Businesses should therefore separately identify additional tax, interest and other exposure instead of assuming that filing GSTR-9 alone regularises every underlying short payment.

Key reconciliation checks before filing an overdue GSTR-9

• Reconcile annual turnover and tax liability with filed GSTR-1 and GSTR-3B returns.

• Reconcile input tax credit with the books, GSTR-3B and available GSTR-2B/portal data.

• Review prior-year transactions reported in the subsequent financial year and the reporting window applicable to that year.

• Identify tax, interest or other liabilities that require payment through DRC-03 rather than merely disclosure in GSTR-9.

• Review HSN reporting and other mandatory annual-return tables before computing liabilities.

• Retain turnover workings used to determine the applicable GSTR-9 late-fee slab and cap.

Can GSTR-9 be revised after filing?

The GST portal’s filing guidance states that once Form GSTR-9 is filed, changes cannot be made in the filed annual return. This makes the review process materially different from a routine monthly compliance exercise. A late filing should not become a rushed filing merely because the return is overdue.

How should finance teams handle an old unfiled annual return?

A practical approach is to first identify the financial year, turnover band, original due date, return status and likely late-fee exposure. Next, reconcile GSTR-1, GSTR-3B, books and ITC. Then isolate any additional tax or interest exposure that may need DRC-03. Only after these steps should the team finalise GSTR-9 and compute portal liabilities.

Where non-filing has already resulted in broader GST compliance problems, the following PGT & Associates guide may also be relevant: https://www.pgtandassociates.com/post/gst-non-filing-notice-gstr-3a-section-46-section-62-assessment.

Frequently asked questions

Is there a late fee for filing GSTR-9 after the due date?

Yes. Section 47(2) provides for late fee on delayed annual returns. Notification No. 07/2023-Central Tax reduces the Central Tax component for specified turnover categories from FY 2022-23 onwards.

What is the GSTR-9 late fee for turnover up to ₹5 crore?

Under Notification No. 07/2023-Central Tax, the Central Tax component is ₹25 per day, capped at 0.02% of turnover in the State or Union territory. The corresponding State/UT GST component must also be considered.

What is the GSTR-9 late fee for turnover above ₹5 crore and up to ₹20 crore?

The Central Tax component is ₹50 per day, capped at 0.02% of turnover in the State or Union territory under Notification No. 07/2023-Central Tax, with the corresponding State/UT component separately relevant.

Does paying late fee remove other GST liabilities?

No. Late fee relates to delayed filing. Tax, interest, penalty or other liabilities are separate matters and must be examined independently.

Can a filed GSTR-9 be revised?

The GST portal states that a filed GSTR-9 cannot be changed after filing. A careful pre-filing review is therefore essential.

Professional takeaway

For businesses with delayed annual returns, the highest-risk mistake is treating GSTR-9 as a simple late-filing exercise. The correct process combines statutory late-fee analysis, turnover verification, annual reconciliation, identification of additional liabilities and documentation of the filing position. Where material mismatches, historic non-compliance or notices exist, professional review before filing can reduce the risk of compounding an existing GST problem.

PGT & Associates assists businesses with GST return regularisation, annual-return reconciliation, late-filing analysis, GST notices and related compliance matters.

Primary references

• Section 44 and Section 47 of the Central Goods and Services Tax Act, 2017.

• Notification No. 07/2023-Central Tax dated 31 March 2023.

• GST Portal official user manual for Form GSTR-9.

Disclaimer: This article is for general professional information only and does not constitute legal or tax advice. GST law, notifications, portal functionality and factual circumstances should be reviewed for the relevant taxpayer and period before taking action.

GST annual return late fee FAQs

What is the GST annual return late fee for GSTR-9?

Section 47(2) provides the statutory annual-return late fee. Notification No. 07/2023-Central Tax reduces the Central Tax component for specified turnover bands from FY 2022-23 onward; the corresponding State/UT component must also be considered. The applicable daily rate and turnover-linked cap should be tested for the taxpayer’s band.

Does the late fee stop when GSTR-9 is filed if GSTR-9C is still pending?

Not where GSTR-9C is applicable. CBIC Circular No. 246/03/2025-GST clarifies that the complete annual return includes both forms in such cases, so the Section 47(2) late-fee period can continue until the required GSTR-9C is also furnished.

Is GSTR-9 late fee the same as GSTR-1 or GSTR-3B late fee?

No. GSTR-9 uses the annual-return framework in Section 47(2). GSTR-1 and GSTR-3B are governed by different return provisions and notification-based concessions, so their rates and caps should not be copied into an annual-return calculation.