One of the mandatory prevailing conditions for availing ITC under section 16(2)is that the tax charged in respect of the supply must be actually reflected in the recipient's GSTR-2B / GSTR-2A which in turn depends upon correct reporting by the supplier in GSTR-1 as B2B.
In your case, the supplier has reported the transaction as B2C instead of B2B for June 2022. Due to this incorrect classification, the ITC does not get auto populated in GSTR-2B resulting in non fulfilment of a statutory condition. Mere payment through banking channels and obtaining a confirmation or certificate from the supplier though evidentiary in nature, cannot substitute statutory compliance.
The tax officer is bound by the provisions of the Act, CBIC circulars and internal instructions which consistently emphasize that ITC eligibility is linked to reflection in GSTR-2B. Hence, discretionary relief at the adjudication stage is unlikely.
Further, appellate authorities, including GSTAT, generally do not grant relief where a clear statutory condition is not met, especially when the lapse pertains to incorrect return filing by the supplier and not merely a procedural defect.
Therefore, unless the supplier rectifies the error by amending GSTR-1 (if legally permissible for the relevant period) and the ITC consequently reflects in GSTR-2B, the probability of relief is remote. Request to approach HC to give direction to allow GST amendment.