A vehicle authentication apparatus including an acquisition unit (65D) configured to acquire information indicating a content of a manipulation on a vehicle from a detection unit mounted on the vehicle; a manipulation determination unit (65E) configured to determine whether a predetermined collaborative manipulation executable by two or more manipulators is performed on the basis of information acquired by the acquisition unit; and an execution unit (65F, 65H) configured to execute a registration process of registering an electronic key of the vehicle in the on-vehicle authentication apparatus or an invalidation process of invalidating the electronic key registered in the on-vehicle authentication apparatus, in a case that it is determined by the manipulation determination unit that the collaborative manipulation is performed.