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Section 39 of CGST Act: Furnishing of Returns

By Tanya Gupta

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Updated on: Dec 26th, 2024

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4 min read

Missed a GST return deadline? Penalties and interest might follow. From GSTR-3B to GSTR-4, the CGST Act, by section 39, sets the deadlines and rules for all taxpayers, ensuring smooth tax reporting. Among the returns associated with the provisions of the said section, GSTR-3B stands out as a summary return mandatory for eligible businesses to file.

What is Section 39 of the CGST Act?

Section 39 is the go-to section for understanding the GST return filing rules. The section explains how taxpayers, ranging from regular businesses to composition scheme holders, need to report monthly or quarterly sales, purchases, tax liabilities, and input tax credit claims. Section 39 of the CGST Act has been structured to provide a standardised framework, allowing registered businesses to file their returns on time and submit accurate information.

Detailed Analysis of Section 39

Let's understand Section 39's requirements for specific filing for various taxpayers.

Sub SectionExplanation
1Monthly filing of GSTR-3B by regular taxpayers, summarising input tax credit, sales, purchases, and tax liabilities.
2Composition scheme taxpayers must file quarterly returns in Form GSTR-4 covering their turnover, purchases and taxes.
3Persons deducting tax under Section 51 must file a monthly return in Form GSTR-7 within 10 days of the following month.
4Input Service Distributors (ISD) must file a monthly GSTR-6 detailing ITC distributed to branches within 13 days of the following month.
5Non-resident taxable persons (NRTPs) must file GSTR-5 within 13 days of the tax period's end or 7 days after registration expiry, whichever is earlier.
6The Commissioner, through written notification, may extend the deadline for filing returns under this section for specified classes of registered persons.
7Registered persons, as specified in sub-section (1), must pay the tax due as per their return by the last date for filing GSTR-3B unless specified otherwise.
8Returns must be filed for each tax period, even if it's a NIL return.
9Suppose an omission or incorrect detail is discovered. In that case, it should be rectified in the next return, subject to interest, within the deadline (30th Nov of the following financial year or annual return date, whichever is earlier).
10A person can only file a return if previous tax period returns or outward supplies under Section 37, i.e. GSTR-1, are filed.
11A return cannot be filed after 3 years from the due date, but the Government may allow exceptions on recommendations.

Insights into Section 39 of the CGST Act: Timelines and Obligations for Filing GST Returns 

Filing returns on time under this section is critical to avoid compliance issues or late fees. Below are the primary deadlines for different categories of GST returns:

FormDeadline
GSTR-3BMonthly, 20th of the following month
GSTR-4Quarterly by composition taxpayers
GSTR-5Monthly, 20th of the following month
GSTR-6ISD reconcile and distributes ITC monthly

Whether GSTR-3B is Actually a Return or Not?

A debatable topic in GST compliance is whether GSTR-3B should be classified as a proper return under Section 39. Initially intended for immediate compliance as a provisional form, GSTR-3B is now most businesses' primary return form. However, over time, it became a key return form for businesses.

In Bharti Airtel Ltd. v. Union of India (2021), the apex court ruled that GSTR-3B is a valid return. The court emphasised that businesses cannot revise GSTR-3B after submission, underscoring its final nature. 

In 2020, the Karnataka High Court observed in the LC Infra Projects Pvt Ltd v. Union of India case that form GSTR-3B is a provisional return for temporarily collecting taxes. The court highlighted that the return filing process under Section 39 must be followed, which signifies that GSTR-3B isn't a statutory return under the GST Act.

In summary, while there were initial doubts, the Supreme Court has declared GSTR-3B to be a return under Section 39. This provides much-needed clarity for businesses and ensures that ITC claims and tax liability declarations made through GSTR-3B remain valid and legally acceptable.  

Consequences of Form GSTR-3B not being a return under Section 39

If GSTR-3B were deemed unofficial under Section 39, the consequences would be severe for businesses. Here's what could happen:

  • ITC Reversals: Without recognising GSTR-3B as a valid return, claiming or reversing input tax credits (ITC) would become challenging.
  • Late Fees and Penalties: Failure to file a recognised return under Section 39 could result in penalties or compliance issues.
  • Increased Compliance Risks: Businesses might face greater scrutiny and risk in audits if GSTR-3B isn't accepted as a legitimate return.

Frequently Asked Questions

Who is required to file returns under GST?

Registered persons under the GST Act, including regular and composition taxpayers, are required to file returns under Section 39.

What are the different types of returns to be filed under Section 39?

Under Section 39 of the CGST Act, forms like GSTR-3B, GSTR-4, GSTR-5, GSTR-6, and GSTR-7 must be filed.

What is the due date for filing GST returns?

For regular taxpayers, GSTR-3B is due by the 20th of the following month.

Can a return, once filed, be revised?

No, currently, GST returns cannot be revised once submitted.

Is Form GSTR-3B a return under Section 39?

Although debated, it's broadly accepted as a return under Section 39.

Is it mandatory to file a NIL return under the CGST Act?

Yes, even if there are no transactions, a NIL return is required.

How can returns be filed under Section 39?

Returns under Section 39 of CGST Act 2017 can be filed online on the GST portal, which ensures a smooth and trackable submission process or using solution like Clear.

About the Author

A Chartered Accountant by profession and a content writer by passion, I've dedicated my career to unraveling the complexities of GST. With a firm belief that learning is a lifelong journey, I've honed my skills in simplifying intricate legal jargon into easily understandable content. The satisfaction of transforming complex tax laws into relatable narratives is what drives me. Read more

Clear offers taxation & financial solutions to individuals, businesses, organizations & chartered accountants in India. Clear serves 1.5+ Million happy customers, 20000+ CAs & tax experts & 10000+ businesses across India.

Efiling Income Tax Returns(ITR) is made easy with Clear platform. Just upload your form 16, claim your deductions and get your acknowledgment number online. You can efile income tax return on your income from salary, house property, capital gains, business & profession and income from other sources. Further you can also file TDS returns, generate Form-16, use our Tax Calculator software, claim HRA, check refund status and generate rent receipts for Income Tax Filing.

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