The answer to your ques. depends on the fact that to whom the freight is being paid?.
If the transporter is a resident,then, section 194C will be applicable as it covers transort charges paid for transport of goods/passengers by ANY mode of transport.
However, if freight is being paid to a Non-resident,then, Section 44BB & section 172 becomes applicable. TDS on NR is deducted u/s 195. Section 44BB is for calculation of income & S.172 is for recovery of tax. Section 172 specifically overrides whole of the income tax i.e. NR engaged in shipping business need not pay any advance tax & TDS.
Hence,in case of NR transporter, NO TDS will be deducted u/s 195.
In case of Indian transporter - TDS u/s 194C
In case of NR transporter - NO TDS