Whether the tax payable under GST Act has to be paid to the Central Government or the State Government?

As per section 39(7), the tax payable as per return has to be paid to the ‘Government’ on or before the due date for filing the return. Section 2(53) of the CGST Act defined ‘Government’ to mean the Central Government. Further, as per Section 2(9) of the IGST Act, the term ‘Government’ has been defined to mean the Central Government.
Therefore, in respect of CGST and IGST taxes, the tax has to be paid to the credit of the Central Government. In respect of SGST, the tax has to be paid to the credit of the State Government

(ICAI FAQ PUBLICATIONS 06-09-2017 RETURNS : FAQ NO. 26)