An electronic key registration system includes a controller of a communication subject, an initial electronic key that communicates with the communication subject and has an initial encryption key generation code, an additional electronic key that communicates with the communication subject, and an information center including an additional encryption key. The initial electronic key holds an initial encryption key generated from the initial encryption key generation code and a logic. The controller holds the logic and identification information of the communication subject. The controller acquires the initial encryption key generation code from the initial electronic key, generates an initial encryption key from the initial encryption key generation code and the logic held by the controller, and stores the initial encryption key. The information center sends the additional encryption key to the additional electronic key or the controller through a network.