It would have been better if you had also explained your designation and the reason for asking the question.
But assuming you are working in the contract cell of a factory, it would depend on the terms of the contract you have signed. You need to check with your Legal Head or General Counsel. In general, the contracts says x amount for salary, y% as administration fee or commission or service charge and all statutory dues. So if the statutory dues are NIL, the same needn't be paid and can be deducted from the bill.
Logically, the money belongs to the company as it is the company (Principal Employer) who is paying the Statutory dues. Your contractor seem to be profiteering.