Understanding GST Late Fees Under Section 47: Provisions, Amendments & Compliance Guide

Section 47 of the CGST Act, 2017, governs the levy of late fees for delays in filing GST returns and has evolved significantly since its implementation to enhance compliance and offer taxpayer relief. Initially imposing a daily fee of ₹100 (₹50 CGST + ₹50 SGST) per return, capped at ₹5,000, it now features a tiered fee structure based on turnover and return type, including GSTR-1, GSTR-3B, GSTR-8, GSTR-10, and annual returns like GSTR-9/9C.

Amendments in 2022 refined its scope, notably excluding GSTR-2 and adding TCS statements (GSTR-8), while late fees for annual returns now vary based on turnover, with capped percentages. Though generally payable in cash and auto-calculated on the GST portal, periodic amnesty schemes provide relief from high penalties. Distinct from interest on unpaid tax, late fees under Section 47 reinforce timely GST compliance.

Understanding GST Section 47: The Levy of Late Fee and Its Evolution

Section 47 of the Central Goods and Services Tax (CGST) Act, 2017, plays a crucial role in ensuring timely compliance under the GST regime by levying a late fee for delayed filing of various returns and statements. This section, which came into force on July 1, 2017, has undergone several amendments and clarifications since its inception, aiming to streamline compliance and provide relief to taxpayers under specific circumstances.

Section 47(1): Late Fee for Outward Supplies Details and Returns

Section 47(1) deals with the late fee for failure to furnish details of outward supplies and certain returns by their respective due dates.

Original Provision: Initially, Section 47(1) stipulated a late fee of one hundred rupees for every day of delay for failing to furnish:

1. Details of outward supplies under Section 37 (GSTR-1)
2. Details of inward supplies under Section 38 (GSTR-2 – which was later suspended/omitted)
3. Returns under Section 39 (e.g., GSTR-3B)
4. Returns under Section 45 (Final Return – GSTR-10)

This daily late fee was subject to a maximum amount of five thousand rupees.

Amendments by Finance Act, 2022 (Effective October 1, 2022): Significant changes were introduced to Section 47(1) by the Finance Act, 2022, with effect from October 1, 2022, as notified by Notification No. 18/2022-Central Tax, S.O. 4569(E), dated 28.09.2022:

• The words “or inward” (referring to inward supplies under Section 38) were omitted. This aligns with the changes made to Section 38 itself, moving away from the earlier concept of two-way communication in return filing (GSTR-2, GSTR-3).
• The words and figures “or section 38” were also omitted.
• A new addition was made: “or section 52” was inserted after the words and figures “section 39 or section 45.” This means that the late fee provisions of Section 47(1) now also apply to the delayed filing of the TCS (Tax Collected at Source) statement by E-commerce Operators under Section 52 (GSTR-8).

Current Late Fee Structure for GSTR-1 and GSTR-3B (and GSTR-8, GSTR-10): While the base rate remains Rs. 100 per day (Rs. 50 under CGST and Rs. 50 under SGST), the maximum late fee for GSTR-1 and GSTR-3B has been rationalized over time based on the taxpayer’s aggregate turnover:

Note: For GSTR-8 (TCS statement) and GSTR-10 (Final Return), the general late fee of Rs. 200 per day (Rs. 100 CGST + Rs. 100 SGST) applies, with a maximum of Rs. 10,000 (Rs. 5,000 CGST + Rs. 5,000 SGST) for GSTR-8 and no specified maximum limit for GSTR-10 (though often capped at Rs. 10,000 in practice for practical purposes).

Section 47(2): Late Fee for Annual Return (GSTR-9/GSTR-9C)

Section 47(2) specifically addresses the late fee for failing to furnish the annual return required under Section 44 by the due date. The annual return includes FORM GSTR-9 and, where applicable, the self-certified reconciliation statement in FORM GSTR-9C.

Provision: Any registered person who fails to furnish the return required under section 44 by the due date shall be liable to pay a late fee of one hundred rupees for every day during which such failure continues. This daily late fee is subject to a maximum amount calculated at a quarter percent (0.25%) of his turnover in the State or Union territory.

Important Clarifications and Amendments for GSTR-9/GSTR-9C:

Combined Late Fee: The CBIC has clarified that the late fee under Section 47(2) is leviable for the delay in furnishing the complete annual return, which includes both FORM GSTR-9 and FORM GSTR-9C (where required). The late fee is not separately leviable for delayed furnishing of GSTR-9 and GSTR-9C; rather, it is calculated from the due date of the annual return until the date of furnishing the complete annual return.

Changes in Maximum Late Fee for GSTR-9 from FY 2022-23 onwards:

• Up to Rs. 5 Crore Turnover: Rs. 50 per day (CGST + SGST) with a maximum of 0.04% of turnover in the State/UT (0.02% each under CGST and SGST Act).
• Between Rs. 5 Crore and Rs. 20 Crore Turnover: Rs. 100 per day (CGST + SGST) with a maximum of 0.04% of turnover in the State/UT (0.02% each under CGST and SGST Act).
• Above Rs. 20 Crore Turnover: Rs. 200 per day (CGST + SGST) with a maximum of 0.50% of turnover in the State/UT (0.25% each under CGST and SGST Act).

Amnesty Schemes and Waivers: The government has periodically introduced amnesty schemes to provide relief for delayed filing of GSTR-9/9C for past financial years. For instance, for financial years up to FY 2021-22, the late fee for GSTR-9 was Rs. 100 per day per Act (total Rs. 200 per day) subject to a maximum of 0.25% of turnover per Act (total 0.50%). Recent amnesty schemes (e.g., in 2023 and ongoing in 2024-2025) have offered waivers or reduced maximum late fees for pending GSTR-9 and GSTR-9C filings for specific financial years, provided they are filed by a certain deadline. It’s crucial to check the latest notifications for applicable amnesty schemes.

General Points on Late Fee Levy

Payment in Cash: Late fees must generally be paid in cash and cannot be offset against available Input Tax Credit (ITC) in the electronic credit ledger.

Auto-calculation on Portal: The GST portal typically auto-calculates the late fee once a return is filed after the due date.

Separate Levy for CGST and SGST/UTGST: The daily late fee and maximum limits are typically specified per Act (CGST Act and respective SGST/UTGST Act). Therefore, a late fee of Rs. 100 per day implies Rs. 50 under CGST and Rs. 50 under the relevant State/Union Territory GST Act.

Interest vs. Late Fee: It’s important to distinguish between late fee and interest. Late fee is levied for delay in filing the return, while interest (usually 18% per annum) is charged on the outstanding tax liability for delayed payment of tax.

In conclusion, Section 47 of the CGST Act is a critical provision for enforcing compliance with GST return filing timelines. Taxpayers must be aware of its provisions, including the recent amendments, and stay updated on any amnesty schemes or waivers announced by the government to avoid or mitigate late fee liabilities. Timely filing of returns is paramount to ensure smooth GST operations and avoid financial penalties.

FAQs on Section 47 of the CGST Act

What is Section 47 of the CGST Act?
Section 47 of the CGST Act deals with the levy of late fees for delayed filing of GST returns and statements.

When did Section 47 come into effect?
Section 47 came into force on July 1, 2017, with the introduction of the GST regime in India.

Which returns are covered under Section 47(1)?
Section 47(1) applies to returns like GSTR-1, GSTR-3B, GSTR-8 (TCS return), and GSTR-10 (Final return).

What is the standard late fee rate under Section 47(1)?
The standard rate is ₹100 per day (₹50 under CGST and ₹50 under SGST), subject to prescribed maximum limits.

Is there a different late fee for nil returns?
Yes, for nil GSTR-1 or GSTR-3B returns, the late fee is ₹20 per day (₹10 CGST + ₹10 SGST), capped at ₹500.

How is the late fee capped based on turnover for GSTR-1 and GSTR-3B?
Capped based on previous year’s turnover: ₹2,000 for ≤ ₹1.5 Cr, ₹5,000 for ₹1.5–5 Cr, and ₹10,000 for > ₹5 Cr.

What is the late fee for GSTR-8 and GSTR-10?
For GSTR-8 and GSTR-10, the fee is ₹200 per day (₹100 CGST + ₹100 SGST), capped at ₹10,000 for GSTR-8. GSTR-10 has no statutory cap but is usually capped at ₹10,000 in practice.

What is Section 47(2) about?
Section 47(2) imposes a late fee for delayed filing of the annual return (GSTR-9/9C) required under Section 44.

How is the late fee for GSTR-9/9C calculated?
₹100 per day (₹50 CGST + ₹50 SGST), capped at 0.25% of turnover in the State/UT.

Have there been any changes in the fee structure for GSTR-9/9C?
Yes, from FY 2022-23, the cap varies: 0.04% of turnover for up to ₹20 Cr turnover, and 0.50% for over ₹20 Cr.

Is late fee the same as interest under GST?
No, late fee is for delay in return filing, while interest (usually 18% p.a.) is for delay in tax payment.

Can late fees be paid using Input Tax Credit (ITC)?
No, late fees must be paid in cash and cannot be set off using ITC.

Does the GST portal auto-calculate late fees?
Yes, late fees are auto-computed when a return is filed after the due date.

Are late fees charged under both CGST and SGST?
Yes, late fees apply under both Acts separately. A ₹100 per day fee implies ₹50 under CGST and ₹50 under SGST.

Has Section 47 been amended?
Yes, several amendments have been made, including in 2022, omitting references to GSTR-2 and including GSTR-8 under its purview.

What was the impact of the Finance Act, 2022 on Section 47?
It removed references to inward supplies (GSTR-2) and added GSTR-8 (Section 52) to the scope of late fee provisions.

Are there any amnesty schemes for late fee waivers?
Yes, the government has periodically announced amnesty schemes reducing or waiving late fees for past returns.

Who needs to file GSTR-9 and GSTR-9C?
All regular taxpayers must file GSTR-9; those with turnover above ₹5 Cr also need to file GSTR-9C.

Is the late fee under Section 47 applicable for delayed GSTR-2?
No, GSTR-2 has been suspended/omitted, and references to it were removed via amendment in 2022.

Can late fee liability be disputed or appealed?
Generally, late fees are statutory and non-discretionary, but relief may be sought through amnesty schemes or legal recourse in exceptional cases.

Do e-commerce operators need to comply with Section 47?
Yes, they are liable for late fees under Section 47(1) if they delay filing GSTR-8 (TCS statement).

What happens if the annual return is filed partially (only GSTR-9 or GSTR-9C)?
Late fee continues to accrue until the complete return (both GSTR-9 and 9C, if applicable) is filed.

Is there a maximum late fee for GSTR-10?
There is no statutory maximum, but in practice, the fee is often capped at ₹10,000.

Does late fee vary between States?
No, the structure is uniform nationwide, but SGST/UTGST portions apply based on the taxpayer’s State or Union Territory.

Where can I check if I have late fee dues?
You can check your liability for late fees on the GST portal under the “Returns” section when filing or previewing a return.