Will an e-commerce operator be liable to pay tax in respect of supply of goods or services made through it, instead of actual supplier

Yes, but only in case of services notified under Sec. 9(5) of the CGST Act, 2017. In such cases tax shall be paid by the electronic commerce operator if such services are supplied through it and all the provisions of the Act shall apply to such electronic commerce operator as if he is the supplier
liable to pay tax in relation to the supply of such services. A similar provision for inter-State supply is provided for in Sec. 5(5) of the IGST Act, 2017. (Refer to Notification No. 17/2017- Central Tax (Rate) and 14/2017- Integrated Tax (Rate) dated 28.06.2017)

(FAQ 5: E-COMMERCE)

Whether a person supplying goods or services through e-commerce operator would be entitled to threshold exemption

  1. No. Section 24(ix) of the CGST Act, 2017 lays down that the threshold exemption is not available to such persons and they would be liable to be registered irrespective of the value of supply made by them.
  2. This requirement is, however, applicable only if the supply is made through such electronic commerce operator who is required to collect tax at source
    under section 52 of the CGST Act, 2017.
  3. However, where the e-commerce operators are liable to pay tax on behalf of the suppliers under a notification issued under section 9 (5) of the
    CGST Act, 2017, the suppliers of such services are entitled for threshold exemption.

(FAQ 4: E-COMMERCE)