GST Returns FAQs — GSTR-1, GSTR-3B, GSTR-9 & Late Fees
7 expert answers on GST Returns Filing (GSTR-1, GSTR-3B & GSTR-9) under GST — eligibility, restrictions, reversals, and recent legal positions.
These questions are drawn from real GST compliance scenarios, litigation, and common queries from practitioners. Answers reflect the law as amended up to Finance Act 2024.
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GSTR-1 is the outward supply statement filed under Section 37 — it lists every invoice (B2B, B2C, export, debit/credit note) issued during the month or quarter. GSTR-3B is the monthly summary return under Section 39 that contains the self-assessed aggregate figures of outward and inward supplies, ITC claimed, and the tax paid. GSTR-1 feeds the recipient's GSTR-2B (ITC auto-population); GSTR-3B is the return on which tax is actually paid. Discrepancies between GSTR-1 and GSTR-3B figures are a primary basis for scrutiny notices under Section 61.
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Under Section 47, the late fee for GSTR-3B is ₹100 per day under the CGST Act and ₹100 per day under the respective SGST/UTGST Act — so ₹200 per day in total. For nil returns (no tax liability), the late fee is ₹20 per day (total ₹40/day). The maximum late fee for annual turnover up to ₹5 crore has been capped by notifications (currently ₹2,000 for nil returns; ₹5,000 or ₹10,000 for others). Late fees cannot be waived by the assessing officer — they must be paid through the GSTN portal.
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The GST system runs automated comparison of GSTR-1 and GSTR-3B data. Significant mismatches trigger a scrutiny notice in Form ASMT-10 under Section 61. The taxpayer must respond within 30 days with an explanation or file an amendment return. Common mismatches arise from: B2C supplies reported in GSTR-1 but missed in GSTR-3B, credit notes not accounted in both returns, and advances received at end of tax period. Failure to satisfactorily explain the mismatch can lead to a best-judgement assessment under Section 62.
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GSTR-9 is mandatory for registered persons with aggregate annual turnover above ₹2 crore. For taxpayers with turnover up to ₹2 crore, it is optional (notified as exempted by the government for most years since 2017). Composition dealers file GSTR-9A instead. The annual return must be filed by 31 December of the following financial year. GSTR-9C (reconciliation statement) is required for taxpayers with turnover above ₹5 crore — it is now self-certified (CA/CMA audit requirement was removed w.e.f. FY 2020-21).
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Post-Finance Act 2022, Section 16(2)(aa) requires that ITC claimed in GSTR-3B must appear in the auto-populated GSTR-2B statement. Claiming ITC beyond GSTR-2B limits exposes the taxpayer to demand and reversal. However, courts have held that GSTR-2B is an auto-generated statement based on supplier filings — if the underlying supply is genuine but the supplier has not filed GSTR-1, the denial of ITC to the bona-fide recipient is being challenged as unconstitutional in several High Courts. The GSTN portal allows taxpayers to claim ITC up to 5% above GSTR-2B as a temporary measure pending reconciliation.
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The Quarterly Return Monthly Payment (QRMP) scheme allows taxpayers with annual aggregate turnover up to ₹5 crore to file GSTR-1 and GSTR-3B quarterly instead of monthly — while paying tax monthly through a Fixed Sum Method (FSM) or self-assessed challan. IFF (Invoice Furnishing Facility) allows large B2B invoices to be uploaded monthly to populate recipients' GSTR-2B even in quarters when GSTR-1 is not due. QRMP reduces compliance burden substantially for small and medium businesses.
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If a registered person fails to file GSTR-3B and does not file within 30 days of receiving a notice under Section 46, the proper officer may proceed to assess the tax liability to the best of his judgement under Section 62 — using available information (GSTR-1 data, e-way bill data, third-party information). The assessment order is passed in Form ASMT-13 and includes tax, interest, and penalty. The order is vacated if the return is subsequently filed within 30 days of service of the ASMT-13 order.