canvat credit on payment to agent

This is related to a shipping company which clear the port related activities with the help of agent at port (port charges, container handling charges, container storage charges etc) Port raise the bill in the name of Agent with service tax. And agent raises the bill for reimbursement of the same without service tax. And therefore currently company not taking the credit of such huge amount paid indirectly as service tax. And we raised the same issue in our audit report. My question is how to explain to department about the same issue. Any case law? or any more suggestions?