By CA Surekha S Ahuja
Complete Procedural, Law-Anchored and Audit-Proof Guide
The annual GST compliance for FY 2024-25 has been significantly reshaped through Notification 16/2025 dated 17 September 2025 and Circular 246/03/2025. With enhanced ITC segmentation, stricter mismatch reporting, and automated scrutiny modules, professionals must adopt a highly structured, defensible approach to GSTR-9 and GSTR-9C to avoid audit objections, interest exposure, and late fee escalation.
Applicability and Filing Framework
GSTR-9 is mandatory for businesses with aggregate turnover above ₹2 crore, while GSTR-9C is mandatory for turnover above ₹5 crore. GSTR-9C is self-certified where applicable. Filing is considered complete only when both forms, where applicable, are successfully submitted.
Certain categories remain exempt, including Input Service Distributors, TDS/TCS deductors, casual taxable persons, non-resident taxable persons, OIDAR suppliers, and foreign airlines (for GSTR-9C only).
Professional Insight: Filing completeness requires careful attention to both thresholds and exempt categories. Misreporting applicability is a common trigger in audits.
Pre-Filing Documentation and Reconciliation
Successful GSTR-9 and GSTR-9C filing starts with robust documentation. Required working papers include:
For GSTR-9:
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GSTR-1, IFF, and GSTR-3B filings for FY 2024-25
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GSTR-2A/2B reconciliation
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Complete sales and purchase registers
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Debit and credit notes
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Import data and reverse charge inward supply (RCM) workings
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HSN summary, including 6-digit for turnover > ₹5 crore and 4-digit for B2B up to ₹5 crore
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Payment challans and DRC-03 where applicable
Additional for GSTR-9C:
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Audited financial statements
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Trial balance and ledger extracts
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GSTIN-wise turnover split by state
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Fixed asset register
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Expense-wise ITC eligibility and mapping sheet
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RCM and import ITC workings
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Management representation letter
Professional Insight: Well-maintained pre-filing documentation forms the backbone of a defensible annual return and GST audit. Each reconciliation should be supported by working papers ready for scrutiny.
Outward Supplies and Turnover Reporting
Outward supplies reported in Tables 4 and 5 must reconcile B2B, B2C, export, and SEZ supplies with GSTR-1. RCM inward supplies in Table 4G must match Tables 6C and 6D to avoid mismatch flags.
Non-taxable, exempt, and nil-rated supplies must be accurately reported. The final turnover is the sum of taxable and exempt supplies, less RCM inward supplies.
Professional Insight: Turnover misreporting is one of the highest scrutiny triggers. All adjustments such as credit notes, advances, unbilled revenue, and deemed supplies should be reflected consistently in books, GSTR-9, and GSTR-9C.
Input Tax Credit (ITC) – The Critical Focus Area
ITC is the most scrutinized area in FY 2024-25. New segmentation requires reporting:
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Table 6A1: ITC of earlier years claimed in the current year
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Table 6A2: Net ITC for the current year
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Table 7A1: Rule 37A reversals for suppliers not filing returns by 30 September
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Table 8H1: Import ITC claimed in the next FY
Reversal checks:
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Rule 37: Non-payment by 180 days
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Rule 37A: Supplier non-compliance
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Rule 42/43: Exempt/blocked use
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Section 17(5): Blocked credits
Reconciliation Process:
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Compare auto-populated GSTR-2B with book ITC
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Ensure first-time claims of next FY are only in Table 8C
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Differences must be classified under Tables 8E or 8F
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Identify ineligible, unclaimed, or excess ITC
Professional Insight: Automated GST scrutiny flags ITC mismatches, overshoot claims, and Rule 37/37A discrepancies. Each claim must have supporting invoices, ledger evidence, and reversal calculations.
Tax Liability and Amendments
Tax, interest, and late fees reported in Table 9 must reconcile with GSTR-3B filings. Negative liability adjustments and additional DRC-03 payments for any under-reported liability must be verified.
Amendments made until 30 November 2025 must be reported under Tables 10–13, which are now mandatory. Ensure all differences due to valuation adjustments under Section 15 are explained.
HSN Reporting
HSN classification is crucial. Six-digit HSN is mandatory for turnover exceeding ₹5 crore, and four-digit HSN for B2B supplies up to ₹5 crore. Inaccurate HSN mapping is a frequent audit trigger.
GSTR-9C – Reconciliation Statement
GSTR-9C begins with audited financial statements and reconciles:
Turnover: Adjust for unbilled revenue, advances, deemed supplies, and credit notes. All differences must have clear explanation.
Tax Liability: Rate-wise reconciliation (5%, 12%, 18%, 28%) and forward/reverse charge matching. Any additional liability must be paid via DRC-03.
ITC: Map book ITC to GSTR-9 figures, identify ineligible, unclaimed, or excess ITC, and maintain expense-wise ITC mappings. This is especially critical for capital goods and blocked credits.
Professional Insight: Reconciliation statements are the first document auditors examine. Every difference must be supported by workings and ledgers.
High-Risk Scrutiny Points
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Turnover mismatches between GSTR-1, GSTR-3B, and books
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ITC mismatches across GSTR-2B, books, and Table 8B
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RCM mismatches between 4G and 6C/6D
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ITC blocked under Section 17(5) claimed erroneously
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Rule 37 and 37A non-compliance
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HSN mismatches
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Wrong reporting between Table 6H and 8C
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Unreconciled liability in Table 9R of GSTR-9C
Automated scrutiny detects overshoot, leakage, amendment patterns, and mismatch trends.
Late Fee, Interest, and Critical Deadlines
Late fees vary by turnover:
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Up to ₹5 crore: ₹50/day, capped at 0.04% of turnover
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₹5–20 crore: ₹100/day
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Above ₹20 crore: ₹200/day, capped at 0.50% of turnover
Interest at 18% applies to additional tax liability.
ITC claims and amendments must be completed by 30 November 2025, and GSTR-9/GSTR-9C filing is due 31 December 2025.
Professional Filing Strategy
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Reconcile GSTR-1 with books and GSTR-3B before starting GSTR-9
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Validate book ITC against GSTR-2B monthly
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Review Rule 37 and Rule 37A supplier compliance
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Ensure RCM liabilities and claims match
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Verify HSN codes across ERP, GSTR-1, and GSTR-9
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Prepare a detailed reconciliation workbook
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Maintain expense-wise and supplier-wise ITC sheets for GSTR-9C
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Save ARN receipts and working files for audit defense
Post-filing, ensure all Tables 12 and 13 are mapped to next year’s ITC claims.
Conclusion
FY 2024-25 introduces unprecedented ITC segmentation, stricter mismatch reporting, and automated scrutiny, making disciplined reconciliation indispensable.
Professionals must adopt a structured, documentation-heavy, and law-compliant approach, ensuring all turnovers, ITC, reversals, amendments, and HSN codes are reconciled.
A fully reconciled and defensible GSTR-9 and GSTR-9C will minimise audit queries, interest exposure, and late fee risk, positioning the business for smooth compliance under the latest GST framework.
