Complete Guide to GST Section 39: Return Filing, Deadlines & Compliance Rules (2025 Update)

Section 39 of the CGST Act, 2017 governs the return filing process under GST, mandating various categories of registered persons—including regular taxpayers, composition dealers, tax deductors, input service distributors, and non-resident taxable persons—to furnish monthly, quarterly, or annual returns in prescribed formats within stipulated timelines. It outlines specific rules for different taxpayer classes, including the QRMP scheme for small taxpayers and mandates nil returns even when no transactions occur.

The section also provides for rectification of errors within a defined period, restricts filing of returns if previous filings are pending, and imposes a three-year limit on furnishing returns. Frequent amendments and government notifications, including deadline extensions, reflect the evolving nature of GST compliance aimed at improving transparency, reducing evasion, and simplifying processes for taxpayers.

GST Section 39: A Comprehensive Guide to Furnishing Returns

Section 39 of the Central Goods and Services Tax (CGST) Act, 2017, effective from July 1, 2017, is the cornerstone of return filing under GST. It mandates various registered persons to furnish periodic returns, ensuring transparency, compliance, and proper tax collection. This section has undergone several amendments since its inception, reflecting the dynamic nature of GST law and the government’s efforts to streamline the return filing process. This article provides a detailed breakdown of Section 39, including its various sub-sections, key amendments, relevant rules, and recent notifications.

Section 39(1): Monthly/Quarterly Returns for Regular Taxpayers

This sub-section, substituted with effect from November 10, 2020, outlines the general requirement for most registered persons to file returns.

Who files: Every registered person, excluding Input Service Distributors (ISD), non-resident taxable persons (NRTP), persons paying tax under Section 10 (composition levy), Section 51 (TDS), or Section 52 (TCS).

Periodicity: Generally, returns are to be furnished for every calendar month or part thereof.

Mode of filing: Electronically.

Information to be furnished: Inward and outward supplies of goods or services or both, input tax credit availed, tax payable, tax paid, and other prescribed particulars.

Form and Manner: As prescribed by rules.

Time and Conditions: Within such time, and subject to such conditions and restrictions as may be prescribed. Notably, this part was further amended (substituted) by the Finance Act, 2025, emphasizing the prescribed nature of deadlines and conditions.

Proviso for Quarterly Filing (QRMP Scheme): The Government, on the recommendations of the Council, may notify certain classes of registered persons who shall furnish a return for every quarter or part thereof, subject to specified conditions and restrictions. This provision facilitates the Quarterly Return Monthly Payment (QRMP) Scheme, offering ease of compliance for smaller taxpayers.

Section 39(2): Annual Returns for Composition Dealers

Who files: Registered persons paying tax under Section 10 (composition levy).

Periodicity: For each financial year or part thereof.

Mode of filing: Electronically.

Information to be furnished: Turnover in the State or Union Territory, inward supplies of goods or services or both, tax payable, tax paid, and such other particulars.

Form, Manner, and Time: As prescribed.

Section 39(3): Monthly Returns for Tax Deductors (TDS)

This sub-section was substituted with effect from November 1, 2024, by the Finance (No. 2) Act, 2024.

Who files: Every registered person required to deduct tax at source under Section 51.

Periodicity: For every calendar month of the deductions made during the month.

Mode of filing: Electronically.

Form, Manner, and Time: As prescribed.

Proviso: The said registered person shall furnish a return for every calendar month whether or not any deductions have been made during the said month, emphasizing the mandatory nature of filing even in nil deduction scenarios.

Section 39(4): Monthly Returns for Input Service Distributors (ISD)

Who files: Every taxable person registered as an Input Service Distributor.

Periodicity: For every calendar month or part thereof.

Mode of filing: Electronically.

Form and Manner: As prescribed.

Due Date: Within thirteen days after the end of such month.

Section 39(5): Monthly Returns for Non-Resident Taxable Persons (NRTP)

Who files: Every registered non-resident taxable person.

Periodicity: For every calendar month or part thereof.

Mode of filing: Electronically.

Form and Manner: As prescribed.

Due Date: Within thirteen days after the end of a calendar month or within seven days after the last day of the period of registration specified under sub-section (1) of section 27, whichever is earlier. It’s important to note that the word “thirteen” was substituted for “twenty” with effect from October 1, 2022.

Section 39(6): Power to Extend Time Limit

Authority: The Commissioner.

Action: May, for reasons to be recorded in writing, extend the time limit for furnishing returns under this section for specified classes of registered persons by notification.

Proviso: Any extension of time limit notified by the Commissioner of State tax or Union territory tax shall be deemed to be notified by the Commissioner.

Section 39(7): Payment of Tax with Return

This sub-section, along with sub-sections (1) and (2), was substituted with effect from November 10, 2020.

• General Rule: Every registered person required to furnish a return under sub-section (1) (excluding those opting for quarterly filing), or sub-section (3) (TDS), or sub-section (5) (NRTP), shall pay the tax due as per such return not later than the last date on which the return is required to be furnished.
• First Proviso (for QRMP Scheme): This proviso was substituted with effect from October 1, 2022. Every registered person furnishing a return under the proviso to sub-section (1) (i.e., quarterly filers) shall pay to the Government, in such form and manner, and within such time as may be prescribed:
  • An amount equal to the tax due taking into account inward and outward supplies, ITC availed, tax payable, and other particulars during a month; OR
  • In lieu of the above, an amount determined in such manner and subject to such conditions and restrictions as may be prescribed. This enables the option to pay 35% of the previous quarter’s tax liability (as per Notification No. 85/2020-Central Tax) or the tax liability paid for the last month of the preceding quarter (for monthly filers shifting to QRMP).
• Second Proviso (for Composition Dealers): Every registered person furnishing a return under sub-section (2) (composition dealers) shall pay to the Government, the tax due taking into account turnover, inward supplies, tax payable, and other particulars during a quarter, in such form and manner, and within such time, as may be prescribed.

Section 39(8): Mandatory Return Filing (Even Nil Returns)

Requirement: Every registered person who is required to furnish a return under sub-section (1) or sub-section (2) shall furnish a return for every tax period whether or not any supplies of goods or services or both have been made during such tax period. This mandates the filing of “nil returns” even if there are no transactions.

Section 39(9): Rectification of Errors

This sub-section was amended with effect from October 1, 2022, with the phrase “Where” substituting “Subject to the provisions of sections 37 and 38, if”.

• Mechanism: If any registered person discovers any omission or incorrect particulars in a furnished return (under sub-sections (1), (2), (3), (4), or (5)), other than as a result of scrutiny, audit, inspection, or enforcement activity by tax authorities, they can rectify such omission or incorrect particulars in the prescribed form and manner, subject to payment of interest.
• Time Limit for Rectification: The proviso to this sub-section was also amended with effect from October 1, 2022. No such rectification is allowed after the thirtieth day of November following the end of the financial year to which such details pertain, or the actual date of furnishing of the relevant annual return, whichever is earlier. Previously, this deadline was “the due date for furnishing of return for the month of September or second quarter.”

Section 39(10): Restriction on Subsequent Returns

This sub-section was proposed to be amended (substituted) with effect from October 1, 2022.

Restriction: A registered person shall not be allowed to furnish a return for a tax period if the return for any of the previous tax periods or the details of outward supplies under sub-section (1) of section 37 for the said tax period has not been furnished by him. This links the filing of GSTR-1 (details of outward supplies) with the filing of GSTR-3B.

Proviso: The Government may, on the recommendations of the Council, by notification, allow a registered person or a class of registered persons to furnish the return, even if they have not furnished returns for one or more previous tax periods or have not furnished GSTR-1 for the said tax period, subject to specified conditions and restrictions.

Section 39(11): Time Limit for Furnishing Returns

This sub-section was inserted by the Finance Act 2023 with effect from October 1, 2023.

Restriction: A registered person shall not be allowed to furnish a return for a tax period after the expiry of a period of three years from the due date of furnishing the said return.

Proviso: The Government may, on the recommendations of the Council, by notification, allow a registered person or a class of registered persons to furnish the return for a tax period, even after the expiry of the said period of three years from the due date, subject to specified conditions and restrictions.

Relevant Rules and Forms under Section 39

To facilitate the implementation of Section 39, various rules and forms have been prescribed:

Rule 61: Form and manner of furnishing of return (e.g., FORM GSTR-3, FORM GSTR-3B).

Rule 61A: Manner of opting for furnishing quarterly return (for QRMP).

Rule 62: Form and manner of submission of statement and return (e.g., FORM GST CMP-08 for composition, FORM GSTR-4).

Rule 63: Form and manner of submission of return by non-resident taxable person (FORM GSTR-5).

Rule 64: Form and manner of submission of return by persons providing OIDAR services (FORM GSTR-5A).

Rule 65: Form and manner of submission of return by an Input Service Distributor (FORM GSTR-6).

Rule 66: Form and manner of submission of return by a person required to deduct tax at source (FORM GSTR-7, FORM GSTR-7A).

Rule 67A: Manner of furnishing of return or details of outward supplies by short messaging service facility.

Rule 68: Notice to non-filers of returns (FORM GSTR-3A).

Rule 82: Details of inward supplies of persons having Unique Identity Number (FORM GSTR-11).

Author Notes and Recent Notifications

The provided Author Notes highlight recent extensions of time limits for various returns, showcasing the Commissioner’s power under Section 39(6):

• Notification No. 05/2025-Central Tax (dated 10.01.2025): Extended GSTR-7 due date for December 2024 till January 12, 2025.
• Notification No. 04/2025-Central Tax (dated 10.01.2025): Extended GSTR-6 due date for December 2024 till January 15, 2025.
• Notification No. 03/2025-Central Tax (dated 10.01.2025): Extended GSTR-5 due date for December 2024 till January 15, 2025.
• Notification No. 02/2025-Central Tax (dated 10.01.2025): Extended GSTR-3B due dates for December 2024 (monthly filers) till January 22, 2025, and for Q3 (Oct-Dec 2024) for QRMP taxpayers based on their principal place of business (January 24th/26th, 2025).
• Notification No. 30/2024-Central Tax (dated 10.12.2024): Extended GSTR-3B due date for October 2024 till December 11, 2024, specifically for registered persons in Murshidabad, West Bengal.
• Notification No. 29/2024-Central Tax (dated 27.11.2024): Extended GSTR-3B due date for October 2024 till November 30, 2024, for registered persons in Manipur.
• Notification No. 85/2020-Central Tax (dated 10.11.2020): Notified the special procedure for quarterly filers under the QRMP scheme for payment of tax in the first and second months of the quarter, effective from January 1, 2021. This notification outlines the 35% payment rule or payment based on the last month’s tax liability for monthly filers.

Key Takeaways and Compliance Implications

Section 39 is a critical provision in the GST framework, ensuring timely and accurate reporting of transactions and tax payments. The various sub-sections cater to different categories of taxpayers, each with specific filing requirements and deadlines. The continuous amendments and notifications underscore the government’s commitment to refining the GST system for better compliance and ease of doing business.

Taxpayers must stay updated with the latest changes and ensure strict adherence to the prescribed forms, manners, and timelines to avoid penalties and ensure seamless GST compliance. The introduction of restrictions on furnishing subsequent returns (Section 39(10)) and the three-year time limit for filing (Section 39(11)) further emphasize the importance of timely and regular compliance.

FAQs on Section 39 of CGST Act

What is Section 39 of the CGST Act?
Section 39 outlines the rules and requirements for filing GST returns by various categories of registered persons under the GST regime.

Who is required to file returns under Section 39(1)?
Regular registered taxpayers, excluding ISDs, non-resident taxable persons, TDS/TCS deductors, and composition dealers, must file monthly or quarterly returns under Section 39(1).

What is the QRMP scheme under Section 39(1)?
The QRMP (Quarterly Return Monthly Payment) scheme allows eligible small taxpayers to file quarterly returns while paying taxes monthly.

What is the filing frequency for composition dealers under Section 39(2)?
Composition dealers must file a quarterly statement using CMP-08 and an annual return using GSTR-4.

Who needs to file returns under Section 39(3)?
Registered persons required to deduct tax at source (TDS) under Section 51 must file GSTR-7 monthly, even if no deductions are made.

Who are Input Service Distributors and what return do they file?
ISDs distribute input tax credit to branches and must file GSTR-6 monthly under Section 39(4).

What is the return requirement for non-resident taxable persons?
NRTPs must file GSTR-5 monthly or for the period of registration, whichever is shorter, under Section 39(5).

Can the due date for filing returns be extended?
Yes, under Section 39(6), the Commissioner has the power to extend return filing deadlines via notification.

When must tax be paid as per Section 39?
Tax must be paid along with the return filing, by the due date. For quarterly filers, monthly payments are required based on actuals or 35% of the previous quarter’s tax.

Is filing a nil return mandatory under Section 39?
Yes, even if no business activity occurred in a tax period, registered persons must file a nil return.

Can errors in filed returns be rectified?
Yes, errors or omissions (not due to audit or enforcement) can be rectified up to November 30 of the following financial year or the filing date of the annual return, whichever is earlier.

Can a return be filed if previous returns are pending?
No, a taxpayer cannot file a return if returns for earlier periods or GSTR-1 for the same period are not filed, as per Section 39(10).

Is there a time limit to file pending returns?
Yes, as per Section 39(11), returns cannot be filed after 3 years from the original due date unless extended by government notification.

What forms are used under Section 39 for return filing?
Common forms include GSTR-3B, GSTR-4, CMP-08, GSTR-5, GSTR-6, GSTR-7, GSTR-11, as applicable to the taxpayer category.

Can taxpayers opt in or out of the QRMP scheme?
Yes, eligible taxpayers can opt in or out of the QRMP scheme as per Rule 61A on a quarterly basis through the GST portal.

What are the consequences of not filing returns under Section 39?
Non-filing can result in penalties, late fees, interest, suspension of GST registration, and restriction on filing future returns.

Are there different forms for different taxpayer types?
Yes, each taxpayer type (e.g., regular, composition, ISD, NRTP, TDS deductor) has a designated return form under GST rules.

How is return filing done electronically?
Returns under Section 39 must be filed through the GSTN portal (www.gst.gov.in) using prescribed forms and timelines.

Can returns be filed through SMS or offline utilities?
Some simplified filings (like nil GSTR-1 or GSTR-3B) can be done via SMS. Offline tools are also available for uploading data.

Where can I find recent updates or extensions related to Section 39?
Recent notifications are published on the CBIC portal and GSTN website. Regular updates include due date extensions and procedural changes.

What is the significance of Notification No. 85/2020?
It introduced the payment options for QRMP taxpayers, including 35% of the previous quarter’s tax or last month’s actual liability.

Are Section 39 return filings linked with other GST sections?
Yes, particularly with Section 37 (GSTR-1) and Section 38, as GSTR-3B filing under Section 39 often depends on submission of outward supplies.

What happens if a taxpayer misses the rectification deadline?
If the deadline (November 30 of the following FY or annual return date) is missed, errors cannot be corrected and may lead to tax disputes.

Is there a difference between monthly and quarterly filing under Section 39?
Yes. Monthly filers submit GSTR-3B every month, while QRMP taxpayers file quarterly but pay taxes monthly in simplified forms.

Does Section 39 apply to OIDAR service providers?
No, OIDAR service providers file returns under Section 39A, using GSTR-5A, as per Rule 64.