Is it permissible for a contractor to take a percentage of the value of spare parts he is asked to provide for a company, knowing that the company is unaware of this?

If you are an agent for the company in purchasing and receiving materials and invoices, it is not permissible for you to benefit yourself (commission or otherwise) without the knowledge of your principal (the company). However, if the company itself handles the purchasing, and you only guide it to the selling stores without being its agent, then it is permissible for you to take a commission from the selling stores, as long as that is not part of your job responsibilities.