Section 44 of CGST Act: GST Annual Returns Clause-by-Clause Explained

By Prajwal Magaji

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Updated on: Dec 29th, 2025

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5 min read

Section 44 of the CGST Act mandates filing of annual return i.e., GSTR 9 for all the taxpayers whose aggregate annual turnover exceeds Rs.2 Crore. The section also mandates filing of GSTR 9C which is a reconciliation statement which is to be filed by taxpayers with sales more This article provides you with an overview on Section 44 of the CGST Act, 2017.

Key Takeaways

  • Section 44 ensures reconciliation of GST transactions of the entire financial year along with reconciliation statements for applicable cases.
  • Filing return under the section provides the GST authorities a total picture of outward and inward supplies, tax paid, and ITC available and helps to match GST returns with books of accounts and detect mismatches. 
  • Perhaps, this helps to ensure that the taxpayers maintain proper records and avoid any misuse of the ITC claimed, for example, fake invoicing, bogus purchases, etc.
  • GSTR 9 summarises the entire financial year’s GST transactions, verifying its accuracy.

What is Section 44 of CGST Act?

Excerpt from the provision CGST Section 44 is given below-

Section 44 of CGST Act

Section 44 of CGST Act

Let’s decode the Section 44-

In simpler terms, every registered person, casual taxable person, non-resident taxable person must submit an annual return, which includes a self-certified reconciliation statement, reconciling the value of supplies declared in the return furnished for the financial year, with the audited annual financial statements for the financial year.

The commissioner has the authority to exempt any class of registered persons from filing an annual return, and the commissioner has exempted any department of the Central Government or a State Government or a local authority, whose books of account are subject to audit by the Comptroller and Auditor-General of India.

The Last date a registered person can file the annual return for a financial year is before the expiry of a period of three years from the due date of furnishing the said annual return.

Annual Return Filing under Section 44

The following are the features of Annual Return Filing as covered in the provision:

  1. Yearly Compliance – Every registered taxpayer (except specific exempt categories) must file the annual return by 31st December of the following financial year, summarising GST activities of the financial year.

Such a summary includes: 

  • Total Outward Supplies (Sales)
  • Total Inward Supplies (Purchases)
  • ITC Availed and Reversed
  • IGST, CGST and SGST paid
  1. Monthly/Quarterly Reconciliation - The outward and inward supplies made every month/quarter must be reconciled with those of GSTR 9. Accordingly, adjustments to be made for all the inputs claimed that do not belong to the particular financial year or amendments made thereof.
  2. Categorise the Adjustments and Reconciliations Made - GSTR 9 contains the details of inputs under different tables:
  • Table 6 contains the details of ITC claimed during the financial year in GSTR 3B of both regular and RCM cases.
  • Table 7 contains the details of ITC reversed or lapsed during the financial year.
  • Table 8 provides the reconciliation of ITC as per GSTR 2A/ 2B with GSTR 3B and books.

Applicability & Thresholds of Section 44

Section 44 applies to every registered taxpayer under GST who is required to file returns during the financial year. Thus, filing of annual return for all the taxpayers, except for the exemptions mentioned below:

  • Input Service Distributor (ISD)
  • GST TDS and TCS Collector
  • Casual Taxable Person
  • Non-Resident Taxable Person (NRTP)
  • Person paying tax under section 52 (Collection of Tax by E-commerce Operators)
  • OIDAR service providers

GSTR 9 - Annual Return for Regular Taxpayer

GSTR 4Annual Return for Composition Taxpayers

GSTR 9BE-commerce Operators TCS Collectors

GSTR 9C - Taxpayers with Sales Turnover more than Rs. 5 crores (Self Certified)

GSTR 9 filing applicability in different situations:

Nil Transactions throughout the yearNil GSTR 9 mandatory.
Cancelled GST during the FYTo be filed within the registered period.
Migrated/Transferred Business To be filed for the period in which the GSTIN was active.

Key Requirements & Compliances

Reporting Requirements – The annual return must include the year-wide details of:

HEADDATA TO BE REPORTED
Outward Suppliestaxable, exempt, nil-rated, exports
Inward Supplies Purchases from registered/unregistered persons
Input tax credit (ITC)Claimed, reversed, lapsed, RCM
Taxes PaidCash and ITC utilisation
HSN-wise SummaryMandatory based on turnover limit
Reverse-charge (RCM)Whether or not from Registered/Unregistered Persons

Penalties for Non-Compliance per day

The annual return is to be filed on or before the due date, which is 31st December of the following financial year. 

If the return is not filed on the due date, then the following late fees will be levied:

  • Rs. 100 per day per Act (CGST ₹100 + SGST ₹100), or
  • Maximum late fees at 0.25% of turnover in the State/UT.

Common Issues & Challenges

  • Elaborate data requirements
    • Bifurcation of ITC into inputs, input services, and capital goods.
    • HSN (Harmonised System of Nomenclature) and SAC (Service Accounting Code) summary for both inward and outward supplies.
  • Input Tax Credit (ITC) Mismatches: This is a major issue, often involving discrepancies between the ITC claimed in GSTR-3B and the amount auto-populated in Table 8A of GSTR-9 (sourced from GSTR-2B/2A). Reasons include:
    • Suppliers failing to file GSTR-1 on time or at all.
    • ITC on inward supplies where the place of supply was reported incorrectly by the vendor.
    • Invoices from a period when the recipient was under the Composition Scheme are not being reflected.
  • Reconciliation: A methodical approach is required to reconcile the data across GSTR 1, 3B, and the auto-populated figures in GSTR 9 with taxpayers’ books of accounts.
  • No Revised Return: GSTR 9, once filed, cannot be revised, but in extreme cases, if revision of the return becomes necessary, then it can be addressed through other means like DRC-03 with additional scrutiny and penalties.

Frequently Asked Questions

Who is required to file a GST annual return under Section 44?

GSTR 9 is required to be filed by all the registered taxpayers whose aggregate turnover exceeds Rs.2 Crores, and GSTR 9C is to be filed by taxpayers with aggregate turnover exceeding Rs.5 Crores and to self-certify.

What forms are filed under Section 44?

  • GSTR 9 - Regular taxpayers with aggregate Turnover of over Rs.2 Crores.
  • GSTR 9A - Composition taxpayers
  • GSTR 9B - E-commerce Operators collecting TCS
  • GSTR 9C - Taxpayers with turnover more than Rs. 5 Crores
What is the difference between Section 44 and Section 39 of the CGST Act?

Section 39 refers to the filing of periodic returns (monthly/quarterly) containing the details of outward and inward supplies. Section 44 requires the filing of an annual return, which is the consolidated summary of the entire financial year's transactions.

What is the timeline for filing the annual return under Section 44?

The annual return (GSTR-9) and reconciliation statement (GSTR-9C, if applicable) must be filed on or before 31st December of the year following the end of the relevant financial year.

What are the penalties for non-filing or incorrect filing under Section 44?

The annual return is to be filed on or before the due date, i.e., 31st December of the following financial year, and if not, late fees of Rs. 100 per day per Act (CGST 100 + SGST 100) or a maximum late fee of 0.25% of turnover in the state/UT.

Can taxpayers revise annual returns filed under Section 44?

No, taxpayers cannot revise returns filed under section 44; therefore, the best strategy is to properly reconcile with accurate workings and file the return.

About the Author
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Prajwal Magaji

Content Writer
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Aspiring Chartered Accountant with 3+ years of hands-on experience in income tax and GST. Having handled everything from the likes of return filings to tax assessments. I'm now bringing that experience into the world of content writing, aiming to make tax less intimidating and more engaging. Read more

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