- 20 Mar, 2026
- Indirect Taxation
- By Kinsmen Indirect Tax Practice Group
Statutory Quick Takeaway (Executive Summary)
What is the GSTR-9C Late Fee Waiver? Through Notification No. 08/2025 – Central Tax, the Central Board of Indirect Taxes and Customs (CBIC) waived late fees payable under Section 47 of the CGST Act, 2017 for registered taxpayers who delayed filing FORM GSTR-9C (Self-Certified Reconciliation Statement) for financial years FY 2017-18 through FY 2022-23. To qualify for the complete waiver, taxpayers must furnish the pending GSTR-9C alongside or subsequent to FORM GSTR-9 on or before the notified statutory deadline.
1. Statutory Context: FORM GSTR-9 vs. FORM GSTR-9C
The Goods and Services Tax (GST) framework enforces annual compliance under Section 44 of the Central Goods and Services Tax (CGST) Act, 2017 read with Rule 80 of the CGST Rules:
- FORM GSTR-9 (Annual Return): A consolidated annual return of all outward supplies, inward supplies, input tax credit (ITC) availed, tax paid, and demands/refunds. Mandatory for taxpayers with aggregate annual turnover exceeding ₹2 Crores.
- FORM GSTR-9C (Reconciliation Statement): A self-certified statement reconciling audited annual financial accounts with figures declared in FORM GSTR-9. Mandatory only for taxpayers whose aggregate turnover exceeds ₹5 Crores in the relevant financial year.
Historically, delayed submission of GSTR-9C attracted cascading daily late fees under Section 47(2), creating substantial financial burdens for manufacturing, trading, and service enterprises that experienced reconciliation delays.
2. Salient Provisions of CBIC Notification No. 08/2025 – Central Tax
The CBIC exercised powers conferred by Section 128 of the CGST Act to grant structural relief. The critical conditions and parameters of this amnesty notification include:
| Parameter | Statutory Provision under Notification 08/2025 |
|---|---|
| Governing Statute | Section 128 read with Section 47 of CGST Act, 2017 |
| Eligible Form | FORM GSTR-9C (Reconciliation Statement) |
| Eligible Tax Periods | FY 2017-18, 2018-19, 2019-20, 2020-21, 2021-22, and 2022-23 |
| Turnover Applicability | Taxpayers with aggregate turnover exceeding ₹5 Crores |
| Prerequisite | FORM GSTR-9 must either have been previously filed or filed concurrently |
| Relief Extent | Late fee exceeding the amount payable under Section 47 is completely waived |
| Refund Restriction | No refund or credit shall be granted for late fees already paid prior to notification |
3. Late Fee Slabs Under Section 47 of the CGST Act
To determine the exact financial exposure and the quantum of relief under the waiver notification, taxpayers must review the statutory late fee structure:
| Taxpayer Turnover Category | Daily Late Fee (CGST + SGST) | Maximum Statutory Cap under Section 47 |
|---|---|---|
| Turnover up to ₹5 Crores | ₹50 per day (₹25 CGST + ₹25 SGST) | 0.04% of turnover in State/UT (0.02% CGST + 0.02% SGST) |
| Turnover > ₹5 Crores to ≤ ₹20 Crores | ₹100 per day (₹50 CGST + ₹50 SGST) | 0.04% of turnover in State/UT (0.02% CGST + 0.02% SGST) |
| Turnover exceeding ₹20 Crores | ₹200 per day (₹100 CGST + ₹100 SGST) | 0.50% of turnover in State/UT (0.25% CGST + 0.25% SGST) |
Under the notification, where GSTR-9 has been filed with applicable fees, the excess fee accumulated on delayed GSTR-9C submission is waived.
4. Practical Compliance Scenarios & Case Analyses
Scenario A: GSTR-9 Filed on Time, GSTR-9C Remained Unfiled
- Facts: An enterprise with ₹12 Crore turnover filed its annual return GSTR-9 for FY 2021-22 before December 31, 2022 (late fee: ₹0). Due to ledger discrepancies, GSTR-9C was not submitted.
- Statutory Relief: By filing GSTR-9C before the notified deadline, the company pays ₹0 late fee. The daily late fee calculation is completely waived.
Scenario B: Delayed GSTR-9 Filed with Late Fee, GSTR-9C Pending
- Facts: A company filed GSTR-9 for FY 2020-21 six months late, paying ₹18,000 late fee, but omitted GSTR-9C. The system calculated an accrued GSTR-9C penalty of ₹1,40,000.
- Statutory Relief: The late fee already paid on GSTR-9 satisfies the requirement. The remaining balance of ₹1,22,000 is waived.
Scenario C: Late Fee Already Paid for GSTR-9C Prior to Notification
- Facts: A taxpayer cleared a ₹65,000 demand order for late GSTR-9C filing in November 2024.
- Statutory Position: Paragraph 4 of Notification 08/2025 explicitly prohibits refunds. The taxpayer cannot claim a cash refund or re-credit to the Electronic Cash Ledger.
5. Step-by-Step Action Checklist for Pending Annual Reconciliations
Taxpayers holding open or defective GSTR-9C notices must complete the following protocol:
[ Step 1: Audit Balance Sheet ]
│ ── Reconcile audited P&L with GST turnover reported in GSTR-1 & GSTR-3B
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[ Step 2: Identify ITC Differentials ]
│ ── Match Table 12 ITC with financial statement expense heads
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[ Step 3: Verify GSTR-9 Status ]
│ ── Ensure Form GSTR-9 is filed and accepted on the GST Common Portal
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[ Step 4: Self-Certify GSTR-9C ]
│ ── Digital Signature (DSC) certification of Tables 5 to 16
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[ Step 5: Portal Submission & Fee Verification ]
│ ── Validate ₹0 fee auto-computation on the GSTN portal6. Frequently Asked Questions (Statutory Compliance FAQ)
Q1: Is CA certification still mandatory for FORM GSTR-9C?
No. Commencing from FY 2020-21 onwards, the requirement of mandatory certification by a practicing Chartered Accountant or Cost Accountant was amended. Taxpayers now self-certify FORM GSTR-9C. However, professional review by a practicing CA is strongly recommended to identify ITC discrepancies and prevent Section 73/74 demand notices.
Q2: What is the turnover threshold above which GSTR-9C must be filed?
FORM GSTR-9C is mandatory only for registered taxpayers whose aggregate PAN-India turnover exceeds ₹5 Crores in the financial year. Taxpayers with turnover up to ₹5 Crores are exempt from filing GSTR-9C.
Q3: Can I file GSTR-9C without filing GSTR-9?
No. FORM GSTR-9C is a reconciliation statement that directly derives its baseline figures from FORM GSTR-9. The GSTN Common Portal does not permit filing GSTR-9C unless FORM GSTR-9 for the respective financial year is successfully filed.
Q4: Does the waiver apply to pending GST demand notices issued by audit officers?
The notification waives statutory late fees for delayed filing under Section 47. It does not waive tax demands, interest under Section 50, or penalties under Section 73/74 arising from irregular ITC claims, bogus billing, or turnover suppression detected during departmental audits.
Q5: How can a taxpayer verify if GSTR-9C late fees have been waived?
Upon logging into the GST Common Portal (www.gst.gov.in), navigate to Services > Returns > Annual Return, select the relevant financial year, and initiate GSTR-9C. The system will display the adjusted late fee liability reflecting the notification waiver.
Professional Indirect Tax Assistance
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