Is paying a sum of money as a commission to an official in a company in exchange for receiving all of his company's customs clearance transactions—with this commission added to the invoice which the company pays in full—considered a bribe, and what is the ruling of Islam on this?

It is incumbent upon the employee and the manager to work for the benefit of the company that has appointed them, because an agent works for the benefit of their principal. Requesting a commission from you in exchange for processing your company's transactions is forbidden, whether you pay it or the company bears it. This is considered among the worst types of betrayal and forbidden bribery. It is not permissible for him to take it, nor is it permissible for you to pay it to him, due to the saying of the Prophet, peace be upon him: "Allah has cursed the one who gives a bribe and the one who takes a bribe." The prevalence of bribery is not an excuse to resort to this path. Therefore, you must reform yourself and adhere to the straight path.