An electronic key registration system comprising: a controller arranged in a communication subject that is communicable with an electronic key; a registration tool that is in wired or wireless connection with the communication subject and configured to perform a registration process for registering the electronic key to the controller of the communication subject when receiving a registration permission signal (Sok); and an information center connected to a network, wherein the registration tool includes an operator ID acquisition unit configured to acquire an operator ID from a key registration operator, and a communication unit configured to send the operator ID to the information center through the network, wherein the information center includes an operator ID verification unit configured to verify the operator ID received from the registration tool, and a permission information notification unit configured to send, when the operator ID is verified, the registration permission signal (Sok) to the registration tool through the network to permit the registration tool to perform the registration process, wherein the registration permission signal (Sok) includes a registration permission command, which permits the registration tool to perform the registration process, and a key ID, which is to be registered, the registration process includes: the registration tool transmitting the registration permission signal (Sok) received from the information center and including the key ID, to the controller of the communication subject, the controller of the communication subject storing the key ID that is received from the registration tool, the controller of the communication subject transmitting the key ID that is received from the registration tool, to the electronic key, and thereafter, the electronic key storing the key ID that is received from the controller of the communication subject. a controller arranged in a communication subject that is communicable with an electronic key; a registration tool that is in wired or wireless connection with the communication subject and configured to perform a registration process for registering the electronic key to the controller of the communication subject when receiving a registration permission signal (Sok); and an information center connected to a network, wherein the registration tool includes an operator ID acquisition unit configured to acquire an operator ID from a key registration operator, and a communication unit configured to send the operator ID to the information center through the network, an operator ID acquisition unit configured to acquire an operator ID from a key registration operator, and a communication unit configured to send the operator ID to the information center through the network, wherein the information center includes an operator ID verification unit configured to verify the operator ID received from the registration tool, and a permission information notification unit configured to send, when the operator ID is verified, the registration permission signal (Sok) to the registration tool through the network to permit the registration tool to perform the registration process, wherein the registration permission signal (Sok) includes a registration permission command, which permits the registration tool to perform the registration process, and a key ID, which is to be registered, the registration process includes: the registration tool transmitting the registration permission signal (Sok) received from the information center and including the key ID, to the controller of the communication subject, the controller of the communication subject storing the key ID that is received from the registration tool, the controller of the communication subject transmitting the key ID that is received from the registration tool, to the electronic key, and thereafter, the electronic key storing the key ID that is received from the controller of the communication subject. an operator ID verification unit configured to verify the operator ID received from the registration tool, and a permission information notification unit configured to send, when the operator ID is verified, the registration permission signal (Sok) to the registration tool through the network to permit the registration tool to perform the registration process, wherein the registration permission signal (Sok) includes a registration permission command, which permits the registration tool to perform the registration process, and a key ID, which is to be registered, the registration process includes: the registration tool transmitting the registration permission signal (Sok) received from the information center and including the key ID, to the controller of the communication subject, the controller of the communication subject storing the key ID that is received from the registration tool, the controller of the communication subject transmitting the key ID that is received from the registration tool, to the electronic key, and thereafter, the electronic key storing the key ID that is received from the controller of the communication subject. the registration tool transmitting the registration permission signal (Sok) received from the information center and including the key ID, to the controller of the communication subject, the controller of the communication subject storing the key ID that is received from the registration tool, the controller of the communication subject transmitting the key ID that is received from the registration tool, to the electronic key, and thereafter, the electronic key storing the key ID that is received from the controller of the communication subject.