If this is a case of Transport of goods by Road, charging of service tax at a rate higher than tha rate specified by government is not correct.
Please confirm whether your case is transport of goods by road or rail. As transport of goods in containers by rail was made taxable vide Notification No. 15/2006-S.T., dated 24.04.2006. Net rate of approximately 3% is applicable as 70% abatement is available on such services. In case the freight shown in the bills is covered under this category, service tax is correctly charged.
For information transport by Govt. Railway (except transport of goods in containers by rail) has been excluded from tax net vide notification No.33/2009-ST. This exemption was withdrawn vide notification 7/2010-ST, but Notification No.7/2010-ST itself has been amended several times for postponement of its effective date. Hence, as of now transport by rail (except transport of goods in containers by rail) will be taxable from April 2012.