Section 49 of GST Act: Payment of tax, interest, penalty and other amounts

Amended and updated notes on section 49 of CGST Act, 2017. Detail discussion on provisions and rules related to payment of tax, interest and penalty.

Amended and updated notes on section 49 of CGST Act, 2017. Detail discussion on provisions and rules related to payment of tax, interest, penalty and other amounts.

Chapter X (Sections 4953A) of the Central Goods and Services Tax Act, 2017 deals with the provisions related to payment of tax. Section 49 of CGST 2017 provides for payment of tax, interest, penalty and other amounts.

Recently, we have discussed in detail section 48 (Goods and services tax practitioners) of CGST Act 2017. Today, we learn the provisions of section 49 of Central GST Act 2017 as amended by the Finance Act 2022.

Section 49 of the Central Goods and Services Tax Act, 2017 has been notified by the Ministry of Finance vide Notification No. 9/2017-Central Tax, G.S.R. 658(E), dated 28.06.2017. This notification was come into force from 1st July, 2017 i.e. the commencement date of section 49 is 1-7-2017.

Name of ActThe Central Goods and Services Tax Act 2017
Enacted byParliament of India
Administered byCentral Board of Indirect Taxes & Customs
Governing bodyGST Council
Number of Chapters21
Number of Sections174
You are reading:
Chapter No.X
Chapter NamePayment of Tax
Section No.49
Section NamePayment of tax, interest, penalty and other amounts
Updated 2024 EditionGST Law Book PDF

Relevant Rules and Forms for GST Section 49:

  • Rule 85: Electronic Liability Register
    • FORM GST PMT-01: Electronic Liability Register of Registered Person
    • FORM GST PMT-04: Application for intimation of discrepancy in Electronic Credit Ledger/Cash Ledger/ Liability Register
  • Rule 86: Electronic Credit Ledger
    • FORM GST PMT-02: Electronic Credit Ledger of Registered Person
    • FORM GST PMT-03: Order for re-credit of the amount to cash or credit ledger on rejection of refund claim
    • FORM GST PMT-04: Application for intimation of discrepancy in Electronic Credit Ledger/Cash Ledger/ Liability Register
  • Rule 86A: Conditions of use of amount available in Electronic Credit Ledger
  • Rule 86B: Restrictions on use of amount available in electronic credit ledger
  • Rule 87: Electronic Cash Ledger
    • FORM GST PMT-03: Order for re-credit of the amount to cash or credit ledger on rejection of refund claim
    • FORM GST PMT-04: Application for intimation of discrepancy in Electronic Credit Ledger/Cash Ledger/ Liability Register
    • FORM GST PMT-05: Electronic Cash Ledger
    • FORM GST PMT-06: Challan for deposit of goods and services tax
    • FORM GST PMT-07: Application for intimating discrepancy relating to payment
    • FORM GST PMT-09: Transfer of amount from one account head to another in electronic cash ledger
  • Rule 88: Identification number for each transaction
  • Rule 89: Application for refund of tax, interest, penalty, fees or any other amount

Section 49 of Central GST – Payment of tax, interest, penalty and other amounts1

Section 49 of CGST Act 2017 shall come into force on 01.07.2017 vide Notification No. 9/2017-Central Tax, G.S.R. 658(E), dated 28.06.2017.

Section 49(1) of CGST Act

Section 49(1): Every deposit made towards tax, interest, penalty, fee or any other amount by a person by internet banking or by using credit or debit cards or National Electronic Fund Transfer or Real Time Gross Settlement or by such other mode and subject to such conditions and restrictions as may be prescribed, shall be credited to the electronic cash ledger of such person to be maintained in such manner as may be prescribed.

Section 49(2) of CGST Act

Section 49(2): The input tax credit as self-assessed in the return of a registered person shall be credited to his electronic credit ledger, in accordance with section 41 or section 43A, to be maintained in such manner as may be prescribed.

[Amendments (omitted) of Section 49(2) are made by the Finance Act, 2022.]

Section 49(3) of CGST Act

Section 49(3): The amount available in the electronic cash ledger may be used for making any payment towards tax, interest, penalty, fees or any other amount payable under the provisions of this Act or the rules made thereunder in such manner and subject to such conditions and within such time as may be prescribed.

Section 49(4) of CGST Act

Section 49(4): The amount available in the electronic credit ledger may be used for making any payment towards output tax under this Act or under the Integrated Goods and Services Tax Act in such manner and subject to such conditions and restrictions and within such time as may be prescribed.

[Amendments (inserted) of Section 49(4) are made by the Finance Act, 2022.]

Section 49(5) of CGST Act

Section 49(5): The amount of input tax credit available in the electronic credit ledger of the registered person on account of––

  • (a) integrated tax shall first be utilised towards payment of integrated tax and the amount remaining, if any, may be utilised towards the payment of central tax and State tax, or as the case may be, Union territory tax, in that order;
  • (b) the central tax shall first be utilised towards payment of central tax and the amount remaining, if any, may be utilised towards the payment of integrated tax;
  • (c) the State tax shall first be utilised towards payment of State tax and the amount remaining, if any, may be utilised towards payment of integrated tax;
  • Provided that the input tax credit on account of State tax shall be utilised towards payment of integrated tax only where the balance of the input tax credit on account of central tax is not available for payment of integrated tax;
  • (d) the Union territory tax shall first be utilised towards payment of Union territory tax and the amount remaining, if any, may be utilised towards payment of integrated tax;
  • Provided that the input tax credit on account of Union territory tax shall be utilised towards payment of integrated tax only where the balance of the input tax credit on account of central tax is not available for payment of integrated tax;
  • (e) the central tax shall not be utilised towards payment of State tax or Union territory tax; and
  • (f) the State tax or Union territory tax shall not be utilised towards payment of central tax.

Section 49(6) of CGST Act

Section 49(6): The balance in the electronic cash ledger or electronic credit ledger after payment of tax, interest, penalty, fee or any other amount payable under this Act or the rules made thereunder may be refunded in accordance with the provisions of section 54.

Section 49(7) of CGST Act

Section 49(7): All liabilities of a taxable person under this Act shall be recorded and maintained in an electronic liability register in such manner as may be prescribed.

Section 49(8) of CGST Act

Section 49(8): Every taxable person shall discharge his tax and other dues under this Act or the rules made thereunder in the following order, namely: ––

  • (a) self-assessed tax, and other dues related to returns of previous tax periods;
  • (b) self-assessed tax, and other dues related to the return of the current tax period;
  • (c) any other amount payable under this Act or the rules made thereunder including the demand determined under section 73 or section 74.

Section 49(9) of CGST Act

Section 49(9): Every person who has paid the tax on goods or services or both under this Act shall, unless the contrary is proved by him, be deemed to have passed on the full incidence of such tax to the recipient of such goods or services or both.

Explanation: For the purposes of this section, —

  • (a) the date of credit to the account of the Government in the authorised bank shall be deemed to be the date of deposit in the electronic cash ledger;
  • (b) the expression, —
    • (i) “tax dues” means the tax payable under this Act and does not include interest, fee and penalty; and
    • (ii) “other dues” means interest, penalty, fee or any other amount payable under this Act or the rules made thereunder.

Section 49(10) of CGST Act

Section 49(10): A registered person may, on the common portal, transfer any amount of tax, interest, penalty, fee or any other amount available in the electronic cash ledger under this Act, to the electronic cash ledger for,––

  • (a) integrated tax, central tax, State tax, Union territory tax or cess; or
  • (b) integrated tax or central tax of a distinct person as specified in sub-section (4) or, as the case may be, subsection (5) of section 25,

in such form and manner and subject to such conditions and restrictions as may be prescribed and such transfer shall be deemed to be a refund from the electronic cash ledger under this Act:

Provided that no such transfer under clause (b) shall be allowed if the said registered person has any unpaid liability in his electronic liability register.

[Amendments (Substituted) of Section 49(10) are made w.e.f. 5th July 2022 by the Finance Act, 2022 vide GST Notification No. 9/2022.]

Section 49(11) of CGST Act

Section 49(11): Where any amount has been transferred to the electronic cash ledger under this Act, the same shall be deemed to be deposited in the said ledger as provided in sub-section (1).

[Sub-section (11) of section 49 were inserted by the Finance (No. 2) Act, 2019 w.e.f. 1-Jan-2020 vide 01/2020-Central Tax]

Section 49(12) of CGST Act

Section 49(12): Notwithstanding anything contained in this Act, the Government may, on the recommendations of the Council, subject to such conditions and restrictions, specify such maximum proportion of output tax liability under this Act or under the Integrated Goods and Services Tax Act, 2017 which may be discharged through the electronic credit ledger by a registered person or a class of registered persons, as may be prescribed.

[Amendments (inserted) of Section 49(12) are made by the Finance Act, 2022]

  1. Section 49 of CGST Act 2017 shall come into force on 01.07.2017 vide Notification No. 9/2017-Central Tax, G.S.R. 658(E), dated 28.06.2017. ↩︎


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