Each Act’s ₹100 a day is waived to ₹25 and charged under two Acts, so ₹50; since June 2021 a ceiling set by turnover stops it, and only cash pays it.
Each Act says ₹100 a day, and a waiver leaves ₹25 of it
Section 47(1) of the CGST Act charges a late fee on a GSTR-1 or a GSTR-3B not furnished by its due date: ₹100 for every day the failure continues, at most ₹5,000. Every State and Union territory GST Act carries the same section, so the fee is charged twice, once as central tax and once as state tax. That is why the portal shows it in two halves, and charges none under integrated tax or cess.
Nobody pays ₹100 a day, because notifications waive most of it. Notification 4/2018-Central Tax does it for the GSTR-1 and Notification 76/2018-Central Tax for the GSTR-3B: everything above ₹25 a day under each Act is waived, and everything above ₹10 a day when the return is nil. ₹25 twice is the ₹50 a day people quote. ₹10 twice is the ₹20 a day for a nil return.
Nil does not mean the same thing for the two returns. A GSTR-3B is nil for this purpose when no central tax is payable in it. A GSTR-1 is nil when there were no outward supplies in the period.
Last year’s turnover sets a ceiling on it
For tax periods from June 2021, Notification 19/2021-Central Tax (for the GSTR-3B) and Notification 20/2021-Central Tax (for the GSTR-1) waive everything above a ceiling. The ceiling follows the aggregate turnover of the previous financial year, which counts every registration under the same PAN, not only the one that is late. Under each Act, and doubled for the fee in all:
- A nil return, whatever the turnover: ₹250, so ₹500 in all. At ₹20 a day it is reached on the 25th day.
- Turnover up to ₹1.5 crore: ₹1,000, so ₹2,000 in all, reached on the 40th day at ₹50 a day.
- Above ₹1.5 crore and up to ₹5 crore: ₹2,500, so ₹5,000 in all, reached on the 100th day.
- Above ₹5 crore: neither notification sets a ceiling, so section 47’s own ₹5,000 stands, ₹10,000 in all, reached on the 200th day.
Working out the fee for one return takes five steps
The portal works it out when the return is filed. By hand, for one return:
- Take the due date: the ordinary one, or the extended one if a notification moved it for that period.
- Count the days from the due date to the day of filing. Filing on the due date is not late, and filing the day after is one day late.
- Multiply the days by ₹25, or by ₹10 for a nil return. That is the fee under one Act.
- Compare it with the ceiling for your turnover and take the smaller of the two.
- Double it for the two Acts.
It stops on the day of filing or at the ceiling, whichever comes first
The fee runs for every day the return is not filed, so it stops in one of two ways: on the day the return is filed, or on the day it reaches its ceiling. Take a seller whose turnover last year was ₹80 lakh, and the GSTR-3B for August 2026, due on 20 September 2026.
Filed on 3 October, it is 13 days late. ₹25 × 13 is ₹325 under each Act, below the ₹1,000 ceiling, so filing is what stopped it, at ₹650 in all.
Filed on 30 November, it is 71 days late. ₹25 × 71 would be ₹1,775 under each Act, which passes the ceiling, so ₹1,000 is charged under each Act and ₹2,000 in all. The ceiling stopped it on the 40th day, and the 31 days after that cost nothing more in late fee.
Reaching the ceiling stops only the fee. The return is still owed, and a late GSTR-3B can make the next GSTR-1 late as well: the portal does not take a GSTR-1 while the GSTR-3B of the period before it is unfiled, and that GSTR-1 then runs a fee of its own.
Each return is its own failure with its own fee. A month in which both the GSTR-1 and the GSTR-3B are late carries two fees, each at ₹50 a day and each with its own ceiling. Periods before June 2021 were covered by a run of amnesties on terms of their own, which neither this guide nor the calculator works out.
It is paid in cash, never from credit
Input tax credit cannot pay a late fee. The credit ledger may be used only for output tax (section 49(4) of the CGST Act), and a late fee is not output tax. On the portal, interest and late fee are paid only from the cash ledger.
A late GSTR-3B carries its fee in Table 5.1. The portal works it out from the due date and the day of filing, and the return is filed only once everything in it, the fee included, has been paid.
A GSTR-1 has no payment step of its own, so nothing is paid on the day it is filed late. The fee is owed all the same under section 47, and like any late fee it can be paid only in cash.
Interest under section 50 is a different charge, on tax paid after its due date: 18% a year, and on a return filed late before any proceedings for that period have begun, it runs only on the part of the tax paid in cash. No ceiling applies to it.
The due date is where the count starts, and it can move
Under the ordinary calendar a monthly GSTR-1 is due by the 11th of the following month and a monthly GSTR-3B by the 20th. Under the QRMP scheme (Notification 84/2020-Central Tax) the quarterly GSTR-1 is due by the 13th of the month after the quarter, and the quarterly GSTR-3B by the 22nd or the 24th according to the state of registration.
The department extends due dates by notification from time to time, sometimes for every registration and sometimes for particular states. When it has, the count starts from the extended date, and a fee worked from the ordinary date is too high. The free calculator fills in the ordinary date for the period and lets you overwrite it for exactly that reason.
Inside fynxIQ, the reminder emails and the calendar apply each extension CBIC has notified once it is entered in fynxIQ’s table of dates, and a moved date names its notification. An extension for some districts only cannot be told from a GSTIN and is not applied, so in such a month a return the calendar lists as overdue may not be late at all.
fynxIQ works the fee out, and leaves charging it to the portal
The free GST late fee calculator runs in your browser with no account and sends nothing. It takes the return, monthly or quarterly filing, the period, the due date, the day of filing, last year’s turnover and whether the return is nil, and shows the fee under central tax and under state tax, the total, whether the ceiling decided it, and the instruments it rests on. For a quarterly GSTR-3B it asks for the state, to tell the 22nd from the 24th. It gives no figure for periods before June 2021.
In the app, fynxIQ emails a reminder up to three days before each GSTR-1 and GSTR-3B date, and each PMT-06 date of a quarterly filer, and none for a return already marked filed; anyone can turn it off in Settings. In a practice workspace, the calendar lists every client’s returns with the overdue ones first, then the next seven days, then the rest, and a return leaves the list once its ARN is recorded. A PMT-06 is a payment, not a return, so it is listed by date and never called overdue.
The GSTR-3B draft does not work out interest or late fee. Table 5.1 is the portal’s figure, and it is paid there. fynxIQ does not file or pay anything.
Try it on your own figures with the free GST late fee calculator.
Which file to download, and from where: the list for each marketplace and the GST portal.
By Raunak Pathak, founder of fynxIQ, who files GST returns on it. Last updated 4 October 2026. This is general information about how GST returns work, not advice about your particular return.