Basically Service Tax is payable either by Service Provider or Service Receiver. In case of GTA, Service Tax is payable by Service Receiver. However, if the Service are provided to individual or HUF, it is the responsibilty of Service Provider t.e Transport Agency to pay Service Tax. In view of provision there is no harm in paying Service Tax by Transport Agency. In your case, if you are not individual or HU, than it is not the responsibilty of Transport Agency to Pay service tax.
There is an exemption that Service Tax is payable on 75 % of the value of Services. Service Receiver (Consignor or consignee) is entitled to avail such exemption, subject to the condition that the Transport Agency has not availed credit of duty paid on inputs and CG used in providing taxable service and Transport Agency has not availed the benefit of Noti.1/2003-ST.
There was an objection by CAG that whether Transport Agency is entitled for such exemption or not. Order under 37 B No.5/1/2007-ST dt.12/03/2007 has clarified that Transport agency iis als entitled to avail such exemption, subject the conditions specified.
With above legal background, Transport Agency could have availed exemption of 75 % of the value of Services. But they have not availed. If they have not recovered Service Tax charged by them in their bills, from you, they can very well file a refund claim, of excess Service Tax paid by them.
Regarding payment of service tax by you (Consignor/consignee), it to inform you that once Service Tax is paid by Transport Agency, you need not to pay again..