Proposed are a storage controller equipped with an encryption function, a data encryption method, and a storage system enabling a user to apply one's desired encryption policy to data received from a computer or the like. This storage controller includes a storage apparatus for storing data from a computer, and a controller for controlling the input and output of data stored in the storage apparatus. The controller has a configuration information management unit for managing configuration information of attributes concerning an encryption function as information for encrypting data, and an encryption execution unit for performing encryption of data from the computer and data stored in the storage apparatus based on the configuration information of attributes concerning the encryption function.