‘Nobody talks about GSTR-9 till a notice hits’: CA flags risks for overlooking GSTR-9 filing

The annual GST return is one compliance requirement most taxpayers rarely discuss—until a notice lands in their inbox. For FY 2024–25, the GST Annual Return (GSTR-9) and the self-certified reconciliation statement (GSTR-9C) must be filed by December 31, 2025. For the majority of GST-registered entities, this marks the final and most critical compliance step for the financial year.

As the deadline approaches, tax practitioners across the country are calling for more time. Professional bodies such as the Bombay Chartered Accountants’ Society (BCAS), the Madhya Pradesh Tax Law Bar Association (MPTLBA) and the Commercial Tax Practitioners Association, Indore (CTPA) have formally urged the government to extend the due date. Their concern: rising compliance pressure driven by changes in return formats, complex reconciliations and recurring technical glitches on the GST portal. According to these bodies, additional time is essential to ensure accurate, error-free filings and to reduce the risk of avoidable disputes.

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.

Kaushik points out that subtle but significant changes this year have tightened scrutiny. Earlier, inconsistencies could remain buried within monthly returns. Now, input tax credit (ITC) that is reclaimed late, reversed earlier or carried forward has distinct visibility. Even ITC pertaining to FY 2024–25 but claimed in early FY 2025–26 is being tracked. “The system is no longer asking, ‘Did you file?’ It’s asking, ‘Does your story make sense?’” he noted.

He also flagged GSTR-9B, a lesser-known annual return meant for e-commerce operators collecting tax at source (TCS). While the form is not yet live, Kaushik warned businesses in the e-commerce ecosystem not to ignore it. Once activated, it will require clean historical data, leaving little room for corrections.

Most GST notices, he stressed, do not arise from fraud but from small mismatches ignored over time—unadjusted advances, missed credit notes, forgotten reverse charge entries or ITC assumed instead of verified. A timely reconciliation of GSTR-1, GSTR-3B, GSTR-2B and books before filing GSTR-9 can prevent such issues. “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.

The December 31 deadline may seem distant, but compliance pressure builds quietly. Those who act early, Kaushik said, sleep better. Those who delay learn the hard way. It is to be noted delayed GSTR-9 filing invites a late fee of Rs 200 per day, Rs 100 each under CGST and SGST, subject to a maximum cap of 0.5% of the taxpayer’s turnover.