A generic supervisory systems architecture is presented for control of two different types of systems; medical systems and industrial systems. It is structured in a hierarchical manner, consisting of a basic-level fuzzy logic controller supervised by a higher level decision-maker, which employs fuzzy logic theory to represent the human expertise used in supervising the plant including both the controller and the process. The supervisory level tasks consist of tuning, generating control rules, fault detection and diagnosis, together with an alarm and monitoring system. The paper is concerned more with the fault detection and diagnosis methods incorporated in the system. Simulation results for a medical system application are presented.