An electronic key registration system includes an electronic key device having a key ID. A controller having a first piece of information is arranged in a communication subject. A registration tool having a second piece of information is configured to write the key ID to the controller. The controller compares, before electronic key registration, the first piece of information and the second piece of information. The controller permits electronic key registration when the comparison indicates that the first piece of information and the second piece of information conform to each other and prohibits the electronic key registration when the comparison indicates that the first piece of information and the second piece of information do not conform to each other.