GSTR-9C: Meaning, Applicability, Due Date, Late Fees, and How to File

Aggregate turnover includes taxable supplies, exempt supplies, exports and interstate supplies made under the same PAN across India. It excludes GST itself and inward supplies on which tax is payable under reverse charge. Looking only at one GSTIN’s taxable sales can therefore give you the wrong answer. 

The threshold says exceeds Rs. 5 crore. If aggregate turnover is exactly Rs. 5 crore, the GSTR-9C requirement does not arise from this threshold.

The ordinary due date is 31 December following the end of the financial year. An extension may change the deadline for a particular year, so check the GST portal before filing. 

You can prepare the reconciliation earlier, but you must file GSTR-9 before submitting GSTR-9C.

GSTR-9C does not have a separate late-fee provision independent of the annual return. Where GSTR-9C is required, late fee under Section 47(2) applies to the complete annual return, comprising GSTR-9 and GSTR-9C.

For annual returns from FY 2022–23 onwards, the applicable daily amount and cap depend on turnover. The figures below combine CGST with an equivalent SGST component:

Notification 07/2023-Central Tax provides the reduced central-tax amount and cap for the first band. The higher band follows the ordinary statutory provisions, subject to applicable notifications. Check the calculation for your financial year and State before relying on an amount. 

Start with your filed GSTR-9 and the financial statements for the same year. Keep the underlying GST records available so you can trace and explain differences.

You may need to upload a balance sheet and profit and loss statement, or an income and expenditure statement, through the filing facility. Keep your reconciliation working papers with the filed return. The GST portal’s GSTR-9C utility guidance covers supporting document uploads. 

Compare each relevant figure in GSTR-9 with your financial statements, then trace any difference to the records behind it.

• Check turnover: Review supplies, exports, exemptions, credit notes and other adjustments that may explain a difference.
• Check tax: Compare the liability reported and paid, including relevant reverse-charge transactions.
• Check ITC: Compare your books with GSTR-3B and GSTR-2B, taking account of the period and purpose of each record.
• Record the explanation:  Keep evidence for material differences and review any additional liability separately.

If the reconciliation reveals tax that needs to be paid, assess the applicable payment procedure, including Form GST DRC-03 where relevant. Entering a difference in GSTR-9C does not itself pay that tax.

File GSTR-9C electronically on the GST portal after filing GSTR-9. The portal enables the GSTR-9C facility once the annual return has been filed. 

• Select the relevant financial year under the portal’s annual return section.
• Review and file GSTR-9.
• Open the GSTR-9C filing facility for the same year.
• Prepare the reconciliation using the available portal process or offline utility.
• Enter the figures and explanations, then upload the required financial statements.
• Review the complete statement, finish taxpayer verification and file it.
• Save the acknowledgement and supporting records.

Follow the instructions displayed for your filing year. The GST portal’s utility manual gives detailed preparation guidance, while portal screens may change. 

GSTR-9 reports annual GST information. GSTR-9C reconciles that return with figures from the taxpayer’s financial statements when the Rs. 5 crore threshold and other filing conditions apply.

If both forms are required, filing GSTR-9 alone does not complete the annual return. 

Please note: Rule 80 of the Central Goods and Services Tax Rules, 2017 sets out the annual-return and reconciliation-statement framework. CBIC Circular No. 246/03/2025-GST clarifies that where GSTR-9C is required, the complete annual return comprises GSTR-9 and GSTR-9C and explains how late fee applies to delayed furnishing of the complete annual return. GST Portal guidance confirms that GSTR-9C can be filed only after GSTR-9 has been filed.

Preparing GSTR-9C involves reconciling turnover, tax paid, and Input Tax Credit (ITC) with the relevant financial and GST records. Businesses may also need to manage other operating expenses while completing their annual compliance requirements. 

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