Sir,
What is your status under Company's Act or Partnership Act? According to rule 2 (d) (B) of Service Tax Rules, 1994“person liable for paying service tax”, -
(B) in relation to service provided or agreed to be provided by a goods transport agency in respect of transportation of goods by road, where the person liable to pay freight is,-
(I) any factory registered under or governed by the Factories Act, 1948 (63 of 1948);
(II) any society registered under the Societies Registration Act, 1860 (21 of 1860) or under any other law for the time being in force in any part of India;
(III) any co-operative society established by or under any law;
(IV) any dealer of excisable goods, who is registered under the Central Excise Act, 1944 (1 of 1944) or the rules made thereunder;
(V) any body corporate established, by or under any law; or
(VI) any partnership firm whether registered or not under any law including association of persons;
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:
Provided that when such person is located in a non-taxable territory, the provider of such service shall be liable to pay service tax.
From your narration I infer that you concern falls under any one of the categories, namely (I) to (VI) above. Therefore the transporter has presumed that you are liable to pay service tax as receiver of the service and hence he has not charged service tax in his bill. Therefore as receiver of the service you have to pay the service tax and you are eligible to take credit of the same provided the service rendered is in respect inward transport of you raw materials/capital goods etc.