How the GST Late Fee is Calculated under Section 47
Section 47(1) of the CGST Act levies a late fee on every registered person who fails to furnish GSTR-1 or GSTR-3B by the statutory due date. The fee accrues automatically on the GST portal from the day after the due date until the return is actually filed — there is no discretionary waiver available to a proper officer; relief is possible only through a specific CBIC amnesty notification issued under Section 128.
The base rate is ₹100 per day under each Act (₹50 total per day: ₹25 CGST + ₹25 SGST) for taxable returns, and ₹20 per day (₹10 CGST + ₹10 SGST) for Nil returns — that is, returns with no outward supply and no tax liability for the period.
CBIC Notification No. 19/2021-Central Tax and 20/2021-Central Tax rationalised the maximum cap by annual aggregate turnover in the preceding financial year, so a small business cannot be charged the full statutory ceiling of ₹5,000 per Act. Section 47(2) separately levies a late fee for delayed filing of the annual return GSTR-9, capped differently by turnover slab under Notification No. 07/2023-Central Tax.
This calculator applies the correct daily rate, counts calendar days of delay (inclusive of the day of filing), and stops the count at the applicable turnover-based cap so the figure matches what the GST portal will actually debit from the Electronic Cash Ledger.
Worked Example: GSTR-3B Filed 40 Days Late
A registered taxpayer with annual turnover of ₹80 lakh (below the ₹1.5 Cr slab) has an outward taxable supply for the tax period and files GSTR-3B 40 days after the due date of 20 June 2026.
Frequently Asked Questions (FAQs)
Is GSTR-3B late fee different from GST interest under Section 50?
Yes. Late fee under Section 47 is a fixed daily penalty for delayed filing of the return itself, charged regardless of whether tax was actually due. Interest under Section 50 is charged separately on any unpaid net cash tax liability for the period. Both can apply to the same delayed return simultaneously — use the GST Interest Calculator for the Section 50 component.
Does the late fee apply if I have no output tax liability for the period?
Yes, but at the reduced Nil-return rate of ₹20/day (₹10 CGST + ₹10 SGST), capped at ₹500, provided the return genuinely has no outward supplies and no tax payable — filing late still attracts this minimum fee.
What is the late fee cap for GSTR-9 (Annual Return)?
Under Notification No. 07/2023-Central Tax, GSTR-9 late fee is capped at ₹20/day (0.02% of turnover in state/UT) up to turnover ₹5 Cr, ₹50/day (0.02%) for turnover ₹5 Cr-₹20 Cr, and ₹100/day (0.05%) above ₹20 Cr turnover — separate from the GSTR-1/3B slabs used in this calculator.
Is the late fee auto-populated or do I need to pay it manually?
The GST portal auto-computes and locks the late fee into the return at the time of filing; it must be paid before the return can be submitted. There is no manual override available to the taxpayer.
Can late fee be waived through an amnesty scheme?
Historically yes — CBIC has issued periodic amnesty notifications under Section 128 (e.g. for pending GSTR-4, GSTR-9, and GSTR-10 returns) capping or waiving late fee for a defined filing window. Check the current CBIC notifications before assuming a waiver applies to your case.
Does the late fee differ for GSTR-4 (Composition taxpayers)?
Yes. GSTR-4 late fee is ₹50/day (₹25 CGST + ₹25 SGST) for taxable filings and ₹20/day for Nil filings, with the total cap fixed at ₹500 (Nil) or ₹2,000 (taxable) under Notification No. 73/2017 as amended — independent of the taxpayer's turnover slab.