In case of Transporter, THE PERSON WHO IS MAKING THE PAYMENT TO THE TRANSPORTER IS LIABLE TO PAY SERVICE TAX.
This has bigger implication from the Departments point of view... and department always catched the neck of these parties since the accounting of transportation charges is recorded in their bookings of accounts. This services could be under many heads, CARTINGS, FREIGHT INWARD/OUTWARDS, TRANSPORTATION EXPENSES...etc.
Now things are pretty safe, if they collect service tax from you and pays it provided they mention the service tax registration number in their invoice.
However, Department would always catch hold of the person who is liable to pay... even though the transporter has paid the service tax. Department have challenged and they have won the case at tribunal as well. i/e because there's no where in the law which allows the transporter to pay tax. See below,
"Consignor or Consignee is liable to pay service tax in relation to taxable service provided by a goods transport agency, where the consignor or consignee of goods is,—
(a) any factory registered under or governed by the Factories Act, 1948 (63 of 1948);
(b) any company 11[formed or registered under] the Companies Act, 1956 (1 of 1956);
(c) any corporation established by or under any law;
(d) any society registered under the Societies Registration Act, 1860 (21 of 1860) or under any law corresponding to that Act in force in any part of India;
(e) any co-operative society established by or under any law;
(f) any dealer of excisable goods, who is registered under the Central Excise Act, 1944 (1 of 1944) or the rules made thereunder; or
(g) any body corporate established, or a partnership firm registered, by or under any law,
any person who pays or is liable to pay freight either himself or through his agent for the transportation of such goods by road in a goods carriage"