The facts are not clear . I presume that the shipping business of Non -Residents are assessed under section. 172 of the Act then the provisions of 194C & 195 of the IT Act have no application in respect of payments made towards freights to foreign companies.

The assessee has to show that the shipping companies to whom payments were made are not only non-residents but also have to show they were assessed under section 172. Only if the assessee is able to prove it, then he will be relieved of from the liability to deduct tax at source from the payments made to them towards freight. Further, the legal position will not change if the payments to the non-resident shipping companies are made through their Indian agents.
The CBDT Circular No.172 dt.19.9.1995 also shows that the provisions of s. 194C and 195 relating to tax deduction at source will not apply to the payments made to non-resident shipping companies only if their income is assessed u/s. 172 of the Act.