Late Returns: Late Fee, Interest, the Three-Year Bar and Notices

A return that misses its due date does not simply become a late return. It sets off several separate things. A late fee starts to run for each day. Interest starts on any tax not paid in time. The later returns behind it cannot be filed, because the portal enforces filing in order. After a notice, an officer may assess the tax without the return. Customers may lose credit, the registration may be suspended or cancelled, and after three years the return can no longer be filed at all. Each consequence has its own provision, and they do not all stop when the return is finally filed.

This guide sets out each consequence, with the amounts currently notified. The individual returns are covered in the earlier guides of this set, and the department’s demand procedure in Notices and Demands: DRC-01A, DRC-01, and Sections 73, 74 and 74A.

What to have ready

Item	Where it comes from
List of unfiled returns, with each due date	Portal, return dashboard; the filing calendar in The GST Returns Calendar
Aggregate turnover for the preceding year (it sets the late fee cap)	Books; the portal shows the figure on the return dashboard
Turnover in the State for the year (it sets the GSTR-9 cap)	Books
Tax due for each pending period, split between credit and cash	Books, GSTR-1, GSTR-2B
Cash ledger balances on and after each due date	Portal, electronic cash ledger
Any GSTR-3A notice, ASMT-13 order, REG-17 or REG-31 notice	Portal, notices and orders
Dates of any proceedings under section 73, 74 or 74A for the periods	Portal; departmental correspondence

Late fee

Section 47(1) applies to a person who fails to furnish details of outward supplies under section 37, or a return under section 39, 45 or 52, by the due date. The person “shall pay a late fee of one hundred rupees for every day during which such failure continues subject to a maximum amount of five thousand rupees”. Section 47(2) sets the fee for the annual return under section 44 at one hundred rupees a day, up to “a quarter per cent. of his turnover in the State or Union territory”.

Under section 128, the Government has waived the fee above lower amounts. Those notifications set the amounts actually payable today. The table gives the central tax figure.

Return	Notification(s)	Per day	Cap
GSTR-3B	76/2018, as amended by 19/2021	Rs 25; Rs 10 where central tax payable is nil	Nil tax payable: Rs 250. Turnover up to Rs 1.5 crore: Rs 1,000. Rs 1.5 crore to Rs 5 crore: Rs 2,500. Above Rs 5 crore: Rs 5,000 (statutory)
GSTR-1	4/2018, as amended by 20/2021	Rs 25; Rs 10 where there are no outward supplies	Nil outward supplies: Rs 250. Then as for GSTR-3B: Rs 1,000, Rs 2,500, Rs 5,000
GSTR-4 (composition, annual)	73/2017, as amended by 21/2021	Rs 25; Rs 10 where central tax payable is nil	Nil tax: Rs 250. Others: Rs 1,000 (2021-22 onwards)
GSTR-5 (non-resident)	5/2018	Rs 25; Rs 10 where central tax payable is nil	Rs 5,000 (statutory)
GSTR-5A (OIDAR)	6/2018	Rs 25; Rs 10 where integrated tax payable is nil	Rs 5,000 (statutory)
GSTR-6 (ISD)	7/2018	Rs 25	Rs 5,000 (statutory)
GSTR-7 (TDS)	23/2024, from 1 November 2024	Rs 25	Rs 1,000; fully waived where no tax was deducted in the month
GSTR-9 (annual), 2022-23 onwards	7/2023	Turnover up to Rs 5 crore: Rs 25. Rs 5 crore to Rs 20 crore: Rs 50. Above Rs 20 crore: Rs 100 (statutory)	0.02 per cent of turnover in the State for the first two classes; 0.25 per cent (statutory) above Rs 20 crore

The caps by turnover for GSTR-3B and GSTR-1 apply “for the tax period June, 2021 onwards or quarter ending June, 2021 onwards”. Turnover means aggregate turnover in the preceding financial year. GSTR-8 (TCS) has been within section 47(1) since 1 October 2022. No notification reducing its fee was found in CBIC’s list of Central Tax notifications as at 11 October 2026, so the statutory amount applies. The same holds for GSTR-10. The late fee for GSTR-9C is governed by Circular No. 246/03/2025-GST and Notification No. 8/2025-Central Tax, and is covered in Filing the Reconciliation Statement, GSTR-9C.

Some points about the table:

• Two fees, one return. These are central tax amounts. The State and Union territory GST Acts carry their own section 47, and the late fee arises under both laws. The portal’s GSTR-3B user manual says there is no late fee “for IGST and CESS”, and disables those columns.
• Nil is defined differently. For GSTR-3B the reduced fee turns on “central tax payable” being nil. For GSTR-1 it turns on there being no outward supplies at all. Neither test is the same as the test for a nil return filed by SMS, explained in Filing Nil Returns by SMS or on the Portal.
• No fee on some items. Circular No. 143/13/2020-GST states that “no late fee is applicable for delay in payment of tax in first two months of the quarter” under QRMP. The portal’s FAQ says no late fee applies to IFF. GSTR-1A has no due date, so it has no late fee either.
• Paid in cash. The ledger rules in section 49 allow the credit ledger to be used only for output tax. Late fee is paid from the cash ledger. The portal’s GSTR-3B manual says the late fee for a late GSTR-3B is “system computed based on the number of days elapsed after the due date”. It is auto-drafted in table 5.1 of the next period’s return.

Interest

Section 50(1) requires a person who fails to pay tax “within the period prescribed” to pay interest “on his own” for the period it remains unpaid. The rate is fixed by Notification No. 13/2017-Central Tax at 18 per cent a year. Under section 50(2), interest runs “from the day succeeding the day on which such tax was due to be paid”.

Interest on the cash portion only. For a return filed late, the proviso to section 50(1) limits interest. It is charged only on “that portion of the tax that is paid by debiting the electronic cash ledger”. Tax met from credit already in the ledger carries none. The Finance Act, 2021 substituted the proviso with effect from 1 July 2017, and Notification No. 16/2021-Central Tax brought the change into force on 1 June 2021. The proviso does not apply where the return “is furnished after commencement of any proceedings under section 73 or section 74 or section 74A in respect of the said period”. The proviso also covers only supplies “declared in the return for the said period”. Tax on a supply of an earlier period, declared in a later return, falls under rule 88B(2) instead: interest runs on the tax that remained unpaid, from its own due date.

Rule 88B sets out the calculation:

• Sub-rule (1). For a late return of the kind just described, interest runs on the cash portion, for the period of delay.
• The proviso to sub-rule (1). This was inserted by Notification No. 12/2024-Central Tax. Cash credited to the ledger “on or before the due date”, and left there until it is debited when the return is filed, is excluded.
• Sub-rule (2). In all other cases, interest runs on the tax unpaid, from the due date to payment.
• Sub-rule (3). For credit wrongly availed and utilised (section 50(3)), interest runs from the date of utilisation to reversal.

What the portal now does. The GST Network’s advisory on interest collection in GSTR-3B (30 January 2026) describes the changes. From the January 2026 tax period, interest on a delayed GSTR-3B is auto-populated in table 5.1 of the next return. The formula is:

“(Net Tax Liability – Minimum Cash Balance in ECL from due date to date of debit) × (No. of days delayed / 365) × Applicable Interest Rate”

The formula follows the proviso to rule 88B(1). The advisory states that the auto-populated amount “is only the minimum interest” and cannot be reduced, although it may be increased. It also states that where the last GSTR-3B of a cancelled registration was filed late, the interest is collected through the final return, GSTR-10. A later advisory (16 April 2026) dealt with interest wrongly calculated for February 2026 and auto-populated in the March 2026 return, and described a recomputation. The portal’s “tax liability breakup” now requires the filer to confirm, period by period, tax of earlier periods paid in the current return. The advisory of 16 March 2026 dates this from the February 2026 tax period.

For quarterly filers, interest on the monthly PMT-06 deposits follows Circular 143/13/2020-GST, explained in The QRMP Scheme.

The notice for non-filing: GSTR-3A

Section 46 provides that where a registered person fails to furnish a return under section 39, 44 or 45, “a notice shall be issued requiring him to furnish such return within fifteen days”. Rule 68 prescribes FORM GSTR-3A for this, and extends it to section 52 statements.

The form says three things. If the return is not filed within fifteen days, the tax liability “may be assessed u/s 62”. No further communication will be issued before assessment. The notice “shall be deemed to have been withdrawn” if the return is filed before the assessment order is issued.

The portal’s FAQ says GSTR-3A is system-generated and appears under notices and orders on the dashboard. It also says that from the 25th of the month an SMS and email are sent to the primary authorised signatory of a person who has not filed GSTR-3B. In an advisory of 20 July 2025 the GST Network acknowledged that GSTR-3A notices for GSTR-4 had been issued in error to some composition taxpayers. These were taxpayers who had already filed, or whose registrations were cancelled before 2024-25, and the advisory asked them to ignore the notices.

Best-judgment assessment: section 62

Where the return is still not filed after the section 46 notice, section 62(1) allows the proper officer to “assess the tax liability of the said person to the best of his judgement taking into account all the relevant material which is available or which he has gathered”. The section applies to returns under section 39 and 45, not to the annual return. The order must issue within five years of the due date of the annual return for the year concerned. It is in FORM GST ASMT-13, under rule 100(1).

The order can be undone by filing. Under section 62(2), where the person “furnishes a valid return within sixty days of the service of the assessment order”, the order “shall be deemed to have been withdrawn”. From 1 October 2023 a further sixty days are available “on payment of an additional late fee of one hundred rupees for each day of delay beyond sixty days”. In either case “the liability for payment of interest … or for payment of late fee under section 47 shall continue”. A valid return is defined in section 2(117) as one “on which self-assessed tax has been paid in full”. A return filed without paying the tax does not withdraw the order.

The three-year bar

The Finance Act, 2023 added the same bar to four provisions:

• section 37(5) for GSTR-1;
• section 39(11) for returns under section 39 (GSTR-3B, GSTR-4, GSTR-5, GSTR-6 and GSTR-7);
• section 44(2) for the annual return; and
• section 52(15) for the TCS statement.

Each bars filing “after the expiry of a period of three years from the due date”. Each also allows the Government, on the Council’s recommendation, to permit late filing by notification “subject to such conditions and restrictions”. Notification No. 28/2023-Central Tax brought the amendments into force on 1 October 2023.

The portal began enforcing the bar later than the law did. The GST Network has issued three advisories:

• 29 October 2024. It said the change was “going to be implemented in the GST portal from early next year (2025)”.
• 7 June 2025. It said the restriction “will be implemented on the GST portal from July 2025 Tax period”.
• 29 October 2025. It said the restriction “will be implemented on the GST portal from November 2025 Tax period”. It listed the latest periods barred with effect from 1 December 2025: GSTR-1, GSTR-3B, GSTR-5, GSTR-6, GSTR-7 and GSTR-8 for October 2022 (July to September 2022 for quarterly filers); GSTR-4 for 2021-22; and GSTR-9 and 9C for 2020-21.

The bar runs return by return and moves forward each month.

Unbarring on application. The portal’s user manual now describes an “Application for Unbarring Returns” (Services > Returns). It is made to the jurisdictional proper officer, with reasons and up to four documents, and is verified by DSC or EVC. If the officer approves it, the barred returns are opened for 30 days. Returns not filed within that time are barred again. If the application is rejected, the FAQ says it may be made again twice under the same ARN. The manual does not identify the notification under the provisos to sections 37(5), 39(11), 44(2) or 52(15) on which the facility rests. Those provisos give the power to relax the bar to the Government, by notification on the Council’s recommendation, and none was found in CBIC’s list of Central Tax notifications as at 11 October 2026. The source of the officer’s power to unbar is therefore not stated anywhere this guide could find.

Before the bar is reached, the sequence rules apply. Section 37(4) and section 39(10) prevent a return being filed while an earlier one is pending. Section 39(10) also prevents GSTR-3B being filed before that period’s GSTR-1, and rule 59(6) prevents GSTR-1 being filed before the previous GSTR-3B. One unfiled return therefore holds up all the later ones.

Effect on input tax credit

A late return can cost credit in two directions.

The filer’s own credit. Section 16(4) bars credit on an invoice “after the thirtieth day of November following the end of financial year to which such invoice or debit note pertains or furnishing of the relevant annual return, whichever is earlier”. Credit is taken in GSTR-3B, so a return filed after that date cannot take credit on that year’s invoices. A March GSTR-3B filed in December is the usual case. The relaxations in section 16(5) and 16(6) are covered in Input Tax Credit: the Conditions in Section 16(2).

The customers’ credit. A customer’s credit depends on the supplier’s GSTR-1 or IFF reaching its GSTR-2B (section 16(2)(aa)), and on the tax having been paid (section 16(2)©). A supplier’s late GSTR-1 delays the customer’s credit. A GSTR-1 filed after the customer’s section 16(4) date can leave the customer unable to take the credit within that limit.

Effect on registration and other facilities

Cancellation and suspension. Section 29(2)© allows cancellation where a registered person “has not furnished returns for such continuous tax period as may be prescribed”. Rule 21 prescribes the periods. Clause (h) sets “a continuous period of six months” for monthly filers, and clause (i) sets “a continuous period of two tax periods” for quarterly filers. For composition taxpayers, section 29(2)(b) refers to the annual return “beyond three months from the due date”. Under rule 21A(2A) the registration may be suspended at once by an intimation in REG-31. The notice, the reply and the effect of filing the pending returns are covered in Responding to a Notice Proposing Cancellation. Revocation after cancellation is covered in Getting a Cancelled Registration Back.

E-way bills. Rule 138E bars the generation of Part A of an e-way bill for a person who “has Not furnished the returns for a consecutive period of two tax periods”, or the statement of outward supplies “for any two months or quarters”. For a composition taxpayer the trigger is missing CMP-08 for “two consecutive quarters”. The Commissioner may lift the bar on application in EWB-05.

Refunds. The GST Network’s advisory of 10 June 2025 says the portal now allows a refund application only once all GSTR-1 and GSTR-3B returns due up to that date are filed. This follows para 6 of Circular No. 125/44/2019-GST.

Amnesties, as history

Several past schemes reduced late fees or withdrew assessments for those who filed within a window. All of them have closed:

• Notification 76/2018. Waived GSTR-3B late fee in full for July 2017 to September 2018, for returns filed between 22 December 2018 and 31 March 2019.
• Notification 19/2021. Capped GSTR-3B late fee for July 2017 to April 2021 at Rs 500 (Rs 250 for nil tax), for returns filed from 1 June 2021. The window was extended to 30 November 2021 by Notification 33/2021.
• Notification 7/2023. Capped GSTR-9 late fee for 2017-18 to 2021-22 at Rs 10,000, for returns filed from 1 April 2023. The window was extended to 31 August 2023 by Notification 25/2023.
• Notification 2/2023. Did the same for GSTR-4 at Rs 250, with full waiver for nil tax, for returns filed between 1 April and 30 June 2023.
• Notification 6/2023. Treated best-judgment orders served by 28 February 2023 as withdrawn where the return was filed, with interest and late fee, by 30 June 2023. The date was extended to 31 August 2023 by Notification 24/2023.
• Notification 8/2025. Waived GSTR-9C late fee for 2017-18 to 2022-23 above the GSTR-9 late fee, where GSTR-9C was filed by 31 March 2025.

Section 128A, a waiver of interest and penalty on certain demands for 2017-18 to 2019-20, is covered in the guide on notices and demands.

At its 57th meeting on 8 October 2026, the GST Council recommended a further relief. It would waive late fee on a section 39(1) return “for taxpayers with an annual turnover up to Rs. 5 crore in the preceding financial year, if the said delayed return is filed by the end of the month in which it was due”. This is a recommendation in the Council’s press release and has not been notified. The amounts in this guide remain those set out above until it is.

The procedure in order

1. List every unfiled return and its due date. Note any that are close to three years old, since those are barred from the portal (sections 37(5), 39(11), 44(2), 52(15)).
2. File in sequence, oldest first, because sections 37(4) and 39(10) and rule 59(6) block later returns.
3. Pay the tax with the return. Interest at 18 per cent runs on the cash portion from the due date (section 50(1) proviso; rule 88B). Cash already in the ledger by the due date is excluded.
4. Pay the late fee in cash. It is capped by return and turnover under the notifications in the table above.
5. If a GSTR-3A notice has issued, file within fifteen days. If an ASMT-13 order has issued, file a valid return with full tax within sixty days, or within a further sixty days with an additional Rs 100 a day.
6. If a REG-31 or REG-17 notice has issued, file all pending returns and pay the dues, as described in the guide on responding to a notice proposing cancellation.
7. For a return already barred, the portal’s application for unbarring is the route the portal provides.

This guide closes the set on returns. What follows unpaid tax, the department’s demand procedure, is covered in the conceptual guide on notices and demands linked at the start of this guide.