Hello,
May I draw the kind attention of the querist and the expert to the following:
1.The clearance from the Special Economic Zone (SEZ) to Domestic Tariff Area is governed by by the provisions of SEZ law read with the Customs Law. In this regard, clearance from SEZ to DTA is required to be made by filing of Bill of Entry(BoE). In terms of Section 51 of the SEZ Act, 2005, it has an overriding effect on all other laws including the GST Law.
2. GST portal does not populate ITC pertaining to Bill of Entry in the case of import of goods from outside India and import from SEZ ( collectively known referred to as " Import Transactions"). Therefore, ITC balance pertaining to Import Transaction is not appearing in GSTR-2A.
3. Further please refer to the Para 3 of the Circular No. 123/42/2019-GST dated 11/11/2019 issued by the CBIC,which has clarified that ITC of IGST paid in respect of import transactions may be availed without any restrictions under Rule 36(4) of the CGST Rules, 2017, as they are outside the ambit of Section 37(1) of the CGST Act, i.e., not required to be uploaded by the supplier in GSTR-1 return filed by them and therefore they not appear in GSTR-2A of the recipient.
4. I refer here the instruction 9 to GSTR-1 which provides that the supply made by SEZ unit to DTA unit without the cover of BoE is required to be reported in GSTR-1. Therefore any supplies which are under the cover of BoE are not required to be reported in GSTR-1 of SEZ Unit.
5. Ex facie, the department will issue notices for the such possible mismatches. Only the effective explanation needs to be furnished reflecting the factual matrix of each case independently.
Subject experts are requested to throw further bright light on this issue.