Hi Asit! If the service provider in case of GTA service is not liable to pay Service Tax, he can not charge the service tax in the invoice. Further, from your post, it seems that the service receiver has paid the service tax to service provider on the basis of invoice as well as he deposited service tax with government. First, ensure who is liable to pay the service tax. If the service receiver is liable to pay service tax, then service provider should repay the amount to service recepient paid to him and he should reverse the service tax liability.