Is it permissible for an engineer to accept a percentage or a fixed amount from a supplier in exchange for collecting the best price offers and sending them to the purchasing department, knowing that this work is not part of his primary duties and he has no role in selecting the supplier?

It is not permissible for you to take a sum of money from the supplier, because you are an agent for your company in this transaction. An agent of a company is not allowed to take an additional amount from the other party without the permission of his principal. Furthermore, this falls under the category of gifts to employees which are prohibited. It is permissible to take a commission if you are not an agent for your company or if your management has given you permission to do so.