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The CBIC clarifies that late fees under section 47(2) of the CGST Act apply to delays in filing complete annual returns under section 44, which includes both FORM GSTR-9 and GSTR-9C (when required). For taxpayers with turnover exceeding the threshold (currently five crore rupees), the annual return is considered incomplete until both forms are submitted. Late fees accrue from the due date until complete submission, with no separate penalties for each form. For financial years up to 2022-23, excess late fees beyond those applicable until GSTR-9 filing date are waived if GSTR-9C is submitted by March 31, 2025. The Goa government has adopted these clarifications for state GST implementation.
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