Is it permissible for the official in charge of shipping goods to keep a sum of money given to him by one of the transportation companies he deals with, which was not agreed upon beforehand nor requested by him?

This amount falls under employee gifts, which are prohibited unless approved by the employer. The proof for this is the hadith (definition) of Abu Humayd Al-Sa'idi regarding the story of Ibn Al-Lutbiyyah, in which the Prophet, peace and blessings be upon him, said: "Why did you not sit in the house of your father and mother until your gift came to you?" and his saying: "Gifts for workers are ghulul (ill-gotten gain)." The fact that the worker did not request these gifts does not lift the prohibition.