Is it permissible for a head of a government department to keep a gift presented to him because of his position, or is he obligated to deposit its value into the institution's treasury and inform the highest-ranking official?

If you informed the authorized official in your workplace and he approved it for you, then you have discharged your responsibility. Otherwise, it is obligatory to return it to the workplace. Gifts to workers must be placed in the public treasury (Bayt al-Mal), and they have no share in them except with the permission of the Imam (leader). If a worker accepts a forbidden gift, he must return it to its giver. If he does not know who the giver is, he must place it in the public treasury.