Why GSTR-9 Filing Is Often Ignored Until GST Notices Arrive for FY 2024–25

The Annual GST Return is a key compliance demand, which is often overlooked until a departmental notice is issued. For Financial Year 2024-25, the deadline to file the GST Annual Return (GSTR-9) and the self-certified reconciliation statement (GSTR-9C) is December 31, 2025. For most GST-registered entities, this is the final and most significant compliance obligation of the year, serving as the comprehensive reconciliation of all monthly and quarterly filings.

As the filing deadline looms, tax professionals across the country are rallying for an extension. Leading organisations, such as the Bombay Chartered Accountants’ Society, the Madhya Pradesh Tax Law Bar Association, and the Commercial Tax Practitioners Association, have formally urged the government to divest action.

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They point to a perfect storm of obstacles: shifting return formats, complex reconciliation demands, and ongoing GST portal issues. According to these groups, extending the deadline is essential to ensure precise filings and prevent costly disputes down the line.

Chartered accountant Nitin Kaushik has summed up the issue bluntly: "The GST Annual Return is something nobody talks about—until a notice arrives." In a post on X, he said clients routinely ask whether GSTR-9 is truly mandatory, if GSTR-9C can be skipped, or why mismatch notices are issued even after filing monthly returns. "That’s when I realise GST compliance is less about forms and more about discipline," he wrote.

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Kaushik notes that new changes this year have increased scrutiny. Previously, inconsistencies could remain hidden within monthly returns. Now, input tax credit (ITC), which is reclaimed later, previously reversed, or carried forward, is clearly visible. Even the ITC relating to FY 2024–25, but claimed in early FY 2025–26, is being systematically tracked. "The system is no longer asking, ‘Did you file?’ It’s asking, ‘Does your story make sense?’" he noted.

He urgently flagged GSTR-9B, a lesser-known annual return required for e-commerce operators collecting tax at source (TCS). Despite the form not being live yet, Kaushik strongly cautioned businesses in the e-commerce ecosystem not to overlook it. Once activated, it will demand precise historical data, offering minimal opportunity for corrections.

He emphasised that the majority of GST notices are not the result of intentional fraud, but rather the cumulative effect of overlooked discrepancies. Issues such as unadjusted advances, omitted credit notes, forgotten Reverse Charge Mechanism (RCM) entries, or Input Tax Credit (ITC) claimed on assumptions rather than verification often trigger scrutiny.

A proactive, four-way reconciliation between GSTR-1, GSTR-3B, GSTR-2B, and your books of accounts before filing GSTR-9 is the most effective safeguard against these avoidable complications. "Boring compliance is the best kind of compliance," Kaushik said, noting that once GSTR-9 is filed, it cannot be revised, and gaps flagged in GSTR-9C often lead to closure through DRC-03.

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While December 31 may seem far off, compliance obligations have a way of accumulating behind the scenes. As Kaushik aptly notes, taking early action is the best remedy for the stress of year-end filings, as those who delay often face a steep learning curve. Beyond the stress, the financial consequences are immediate: late GSTR-9 submissions incur a daily penalty of ₹200 (₹100 each for CGST and SGST). This penalty adds up quickly, capped only at 0.5% of total turnover, making procrastination a costly business risk.