GST late fee: what a delay costs, and where the cap starts
Late fee under Section 47 is charged per return, per Act: ₹25 under CGST plus ₹25 under SGST, so ₹50 a day for a return that carries tax and ₹20 a day for a nil return. The annual return is different — ₹200 a day, capped at 0.5% of aggregate turnover rather than by slab. The cap is what makes the arithmetic non-obvious: for a taxpayer under ₹1.5 crore turnover the fee stops at ₹2,000, which is 40 days at ₹50, so a delay of three months and a delay of three years cost the same. Above the cap, the only number still moving is the interest, which is 18% a year under Section 50, is charged on the tax rather than the turnover, and has no cap at all. That split — a capped fee and an uncapped interest — is why a long delay is usually an interest problem, not a late-fee problem, and why this calculator shows the two separately instead of adding them into one figure nobody can check.
Frequently asked questions
How is GST late fee calculated?
It is a daily charge from the day after the due date until the day the return is actually filed. For GSTR-1 and GSTR-3B it is ₹50 a day — ₹25 under CGST and ₹25 under SGST — and ₹20 a day for a nil return. The annual return, GSTR-9, is ₹200 a day. The daily figure stops at a cap that depends on your aggregate turnover, so the total is whichever is lower: the days multiplied by the daily rate, or the cap.
What is the late fee for GSTR-3B?
₹50 a day where the return carries tax liability, and ₹20 a day for a nil return. The fee runs from the day after the due date to the date of filing, including both, and is capped at ₹2,000 if turnover is up to ₹1.5 crore, ₹5,000 between ₹1.5 crore and ₹5 crore, and ₹10,000 above ₹5 crore. At ₹50 a day the small-taxpayer cap is reached in 40 days, so a delay of two months and a delay of two years cost the same fee.
What is the late fee for a nil return?
₹20 a day — ₹10 under CGST and ₹10 under SGST — capped on the same turnover slabs as a return with tax. A nil return attracts no interest, because interest under Section 50 is charged on tax paid late and a nil return has none. That makes a late nil return cheap in fee but still worth filing: the portal blocks subsequent returns and eventually the registration itself.
Is there a maximum late fee?
Yes, and it is the number most calculators leave out. For GSTR-1 and GSTR-3B the cap depends on the previous financial year's aggregate turnover: ₹2,000 up to ₹1.5 crore, ₹5,000 from ₹1.5 crore to ₹5 crore, and ₹10,000 above ₹5 crore. For GSTR-9 the cap is 0.5% of aggregate turnover rather than a slab. Relief notifications have reduced these caps for specific past tax periods, so if you are filing for an old period, reconcile against the figure the portal computes.
What is the late fee for GSTR-9?
₹200 a day — ₹100 under CGST and ₹100 under SGST — from the day after the due date until filing, capped at 0.5% of aggregate turnover for the year. Because the cap is a percentage rather than a slab, it is generous at small scale: a business with ₹20 lakh turnover is capped at ₹10,000, which 50 days of delay reaches, while one with ₹2 crore turnover is capped at ₹1,00,000, which takes 500 days. GSTR-9C attracts its own fee on the same basis where it is applicable.
Is interest charged in addition to late fee?
Yes, and the two are separate charges with different rules. Late fee is a fixed daily amount that stops at a cap. Interest under Section 50 is 18% a year on the tax paid late, runs from the day after the due date, and has no cap — so on a large liability the interest overtakes the fee quickly. Interest on excess input tax credit utilised is 24% a year. A calculator that adds a single "penalty" figure is hiding which of the two is actually driving the cost.
Can the GST late fee be waived?
Only by a notification, and only for the periods and taxpayers it names. The COVID-era relief for GSTR-3B and the amnesty schemes for GSTR-9 are examples: they waived fee for returns filed within a window, not for everyone who asked. There is no general power to waive it on request, and the portal computes it automatically when you file. If the delay was caused by a portal outage or a cancelled registration, that is a grievance to raise with the department, not something the return screen will adjust.
Does late fee apply to GSTR-1 as well?
Yes, on the same daily rates and the same turnover caps as GSTR-3B — ₹50 a day, ₹20 for nil, ₹2,000 / ₹5,000 / ₹10,000 by turnover. GSTR-1 is the outward supply statement, so filing it late also delays the buyer's input tax credit appearing in their GSTR-2B, which is a commercial cost on top of the fee. Filing GSTR-1 first and GSTR-3B after it is the usual order for that reason.