This is the practical difficulty faced by most of the assessees.
In normal course, the Manufacturing Company arrange a Freight Forwarder for clearing and forwarding of their goods ( either Export or Import ).
This Freight forwarder used to avail the Services like CHA, Port Authority etc from others. These Service Provider raise the Bills in the name of Freight Forwarder who pays them on behalf of the Company.
After departure/Arrival of the shipment, the Freight Forwarder raises a Single Bill where he mentioned all the relevant Charges paid by him on behalf of the company.
Now the question arises, what about the service tax paid. Since the Bill of the Freight Forwarder doesn't show these ST, the company cann't avail the Cenvat Credit of the Service Tax Paid.
In such cases, you should ask the Freight Forwarder to raise the Bill on account of Company directly and can avail the Cenvat Credit of Service Tax Paid as an Input Service.
If the amount involved in this is very huge then may appoint the different agencies. But this seems to be difficult in view of co-ordination.