The Ministry of Finance has issued a notification relevant for Goods and Service Tax (GST) registered taxpayers who failed to file the annual reconciliation statement through the GSTR-9C form. As per the circular eligible GST taxpayers now have an opportunity to get a waiver of any pending late fees for filing GSTR-9C for FY 2017-18, FY 2018-19, FY 2019-20, FY 2020-21, FY 2021-22 or FY 2022-23. However, there is a catch which is you need to file any pending GSTR-9C on or before March 31, 2025, if you want the benefit of waiver of late fees. The original deadline to file GSTR-9 and GSTR-9C, both for any particular financial year is December 31. While the GSTR-9 annual return can very well be filed without the GSTR-9C return, the law recommends both the returns be filed together. The present notification is relevant for those taxpayers who didn’t follow this recommendation and skipped filing GSTR-9C.
What did the Finance Ministry say about waiver of late fees for filing GSTR-9C after the deadline
“The Central Government on recommendations of the Council, hereby waives the amount of late fees for financial years 2017-18, or 2019-20 or 2020-21 or 2021-22 or 2022-23, which is in excess of the late fee payable under section 47 up to the date of furnishing of FORM GSTR-9 for the said financial year, for the class of registered persons, who were required to furnish reconciliation statement in FORM GSTR-9C along with the annual return in FORM GSTR-9 for the said financial year but failed to furnish the same along with the said return in GSTR-9, and furnish the said statement in FORM GSTR-9C, subsequently on or before the 31st March, 2025. Provided that no refund of late fee already paid in respect of delayed furnishing of FORM GSTR-9C for the said financial years shall be available.
Chartered Accountant Deep Koradia says, “The notification has waived off late fees for filing GSTR-9C, If a taxpayer has filed GSTR-9 on or before the deadline then late fees for GSTR-9C will not be levied now (for FY 2017-18 to 2022-23). Another situation where a taxpayer has filed GSTR-9 after the deadline but paid the late fees then GSTR-9C late fees would not be separately levied. However, in the past the GST department has issued show cause notices (SCNs) for non-payment of late fees for late filing GSTR-9C. Now after this notification a taxpayer can reply to these SCNs and request the GST proper officer to drop the case and give relief from late fees. It is pertinent to mention that if such late fees on GSTR-9C have already been paid, then refund won’t be granted for the same”
Last opportunity to save yourself from GST scrutiny; file pending GSTR-9C by March 31, 2025
Chartered Accountant Bimal Jain, founder, A2Z Taxcorp says, “If a GST registered person fails to use this last opportunity to file GSTR-9C return, after filing year wise GSTR 1 and GSTR 3B return with due reconciliation with GSTR 2A/ GSTR 2B , then, the department at the time of scrutiny of GST Returns, GST Audit, Inspection & Search may initiate a proceedings for any variances in outward supplies and tax payable thereon, GST Credit with its purchase with reverse charge mechanism (RCM) liabilities against that person and may also issue a show cause notice either under section 73 (non-fraud) or section 74 (fraud), as the case may be.”
Jain explains the importance of GSTR-9C. “The GSTR-9C statement acts as a base and is stated to be a self-certified reconciliation statement with annual return (GSTR 9) for the GST authorities to verify the correctness of the GST returns filed by the taxpayers after a self-certification. The department may also interpret non-filing of GSTR-9C as an intention to suppress, misstatement and fraudulent to evade taxes.”Sivakumar Ramjee, Executive Director- Indirect Tax, Nangia Andersen LLP, says, “The late fees of surpassing the amount liable to get paid under section 47 of the CGST Act have been waived for taxpayers who file their pending FORM GSTR-9C by March 31, 2025. Surprisingly it is also clarified that taxpayers who have voluntarily paid the late fee earlier shall not be qualified for any refund. It is advised to the taxpayer to file their outstanding FORM GSTR-9C reconciliation statements on or before March 31, 2025, to benefit from this late fee waiver. The intention is to simplify the compliance load and motivate the timely filing of the due reconciliation statements. It is highly recommended that taxpayers have to take the benefit of the same relief to prevent the additional penalties and ensure the GST statutory compliance.””Failure to file GSTR-9C can, at first, result in a notice to be issued to the taxpayer requiring filing within a specified timeline. Non-compliance can also result in late fees and penalties being imposed on the taxpayer. Additionally, GST audit or assessment proceedings may be initiated against the non-compliant taxpayer whereby the department can invoke allegations of fraud and suppression on the taxpayer,” Kulraj Ashpnani, Partner, Dhruva Advisors LLP said.
Who needs to file GSTR-9C and GSTR-9?
Jain says the applicability of GSTR-9C is determined based on the aggregate turnover of a taxpayer in a financial year. Over the years, the threshold limits and requirements for filing GSTR-9C have undergone changes. Here’s a year-wise breakdown since 2017:
| Financial year | Aggregate Turnover Threshold for GSTR-9C Filing | Certification Requirement |
| 2017-18 | Above Rs 2 crore | Mandatory |
| 2018-19 | Above Rs 5 crore | Mandatory |
| 2019-20 | Above Rs 5 crore | Mandatory |
| 2020-21 | Above Rs 5 crore | Self-certification |
| 2021-22 | Above Rs 5 crore | Self-certification |
| 2022-23 | Above Rs 5 crore | Self-certification |
Source: CA Bimal Jain
2017-18: Taxpayers with an aggregate turnover exceeding Rs 2 crores were required to file GSTR-9C, which had to be certified by a Chartered Accountant (CA) or Cost Accountant (CMA).
2018-19 and 2019-20: The threshold limit for mandatory filing of GSTR-9C was increased to Rs 5 crore. Certification by a CA or Cost Accountant remained mandatory.
2020-21 onwards: While the threshold limit remained at Rs 5 crore, the requirement for certification by a CA or Cost Accountant was removed. Taxpayers could self-certify the GSTR-9C form.
According to Ashpnani from Dhruva Advisors LLP, “In the GST regime, all registered persons, except Input Service Distributors, persons liable to deduct TDS/TCS, casual taxable persons, and non-resident taxable persons, are required to file an annual return in Form GSTR-9 (GSTR-9) and a self-certified reconciliation statement (earlier a CA-certified statement) in Form GSTR-9C (GSTR-9C) by 31st December following the end of the financial year. The threshold for filing GSTR-9 is an annual aggregate turnover of Rs 2 crores (PAN India), while for GSTR-9C, it is Rs 5 crores.”
What is the purpose of filing GSTR-9C?
According to Ramjee, “Filing GSTR-9C, the reconciliation statement, along with the GSTR-9 annual return, is crucial under India’s Goods and Services Tax (GST) laws for taxpayers whose aggregate turnover exceeds Rs 5 crore in a financial year.GSTR-9C is a mandatory filing under Section 44(2) of the CGST Act, 2017, applicable to taxpayers meeting the aforementioned turnover threshold. GSTR-9C reconciles the figures reported in the annual return (GSTR-9) with the taxpayer’s audited financial statements. It helps identify discrepancies, if any, and ensures the accuracy of GST declarations. Failure to file GSTR-9C can attract penalties under Section 125 of the CGST Act, which imposes a general penalty of up to ₹25,000 for non-compliance. State GST laws may impose equivalent penalties, doubling the financial burden. Late filing of GSTR-9C attracts a late fee, which can add to the financial liability of the taxpayer. Non-filing or incorrect filing can trigger scrutiny, audit, or even investigation by GST authorities, leading to prolonged compliance procedures.”
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