How GST late fees and interest actually work
Two separate charges stack on a late GST return, and they run on different rules — conflating them is how most published figures go wrong.
- Late fee — a per-day charge under Section 47 of the CGST Act, split equally between CGST and SGST. For GSTR-1 and GSTR-3B it is a flat ₹50 a day (₹20 for a nil return) with a cap that depends on your turnover in the preceding financial year. GSTR-9 uses its own scale, based on the turnover for the year the return covers, with both the daily rate and the cap rising in steps.
- Interest — 18% per annum under Section 50(1), charged only on the net tax actually paid in cash after ITC is set off, from the due date to the date of payment. It applies to GSTR-3B, where the payment happens — not to GSTR-1, which carries no tax payment of its own.
Watch for any amnesty or waiver notification the government has open at the time you file — these periodically reduce or write off pending late fees for specific return periods, and the portal applies them automatically at filing.