Payment of taxes under gst is linked to debit in electronic cash / credit ledgers.
Section 50 (1) reads as under:
"Every person who is liable to pay tax in accordance with the provisions of this Act or the rules made thereunder, but fails to pay the tax or any part thereof to the Government within the period prescribed, shall for the period for which the tax or any part thereof remains unpaid, pay, on his own, interest at such rate, not exceeding eighteen per cent., as may be notified by the Government on the recommendations of the Council.
2[Provided that the interest on tax payable in respect of supplies made during a tax period and declared in the return for the said period furnished after the due date in accordance with the provisions of section 39, except where such return is furnished after commencement of any proceedings under section 73 or section 74 in respect of the said period, shall be payable on that portion of the tax which is paid by debiting the electronic cash ledger.]"
While proviso allows, subject to conditions specified therein (i.e. except where such return is furnished after commencement of any proceedings under section 73 or section 74), to levy interest only on that portion of the tax which is paid by debiting the electronic cash ledger. But, as per the beginning part of said proviso, one needs to declare such tax liability while filing return (i.e. GSTR-3B) for the tax-period when such liability arise.
However, Section 39 (9) of the CGST Act, 2017 permits 'rectification' subject to certain conditions and but also subject to payment of interest.
So, on plain reading of these provisions, interest is payable. But, there is decent chance for Court (specially, high court) to quash interest-liability on following two grounds:
A. Interest is compensatory in nature and in given situation, Govt. is not deprived of any revenue due to delay in beit in electronic credit ledger;
B. Co-joint reading of proviso to Section 50 (1) read with Section 39 (9) means that there is no delay in paying taxes when ITC ledger balance was sufficient constantly in between tax-period/s.
However, one cannot be certain whether court will go with very strict interpretation of legal provisions / rules or take holistic approach keeping in mind above two grounds.
All above are strictly personal views of mine and the same should not be construed as professional advice / suggestion in any way.