An encrypted control system, an encrypted control method, and an encrypted control program make it possible to further reduce a risk of a cipher key leaking. An input device, a plant-side control device, and a controller are respectively equipped with pseudorandom number calculation units having a common function, are time synchronized, and start a synchronized operation at the same time. Since the encrypted control system is configured in such a manner, it becomes possible to switch a pair of a public key and a private key in synchronization with a control cycle of the entire control system. Consequently, it becomes possible to instantaneously and definitely detect intervention in the control system by a malicious third party.