Elementary siphons have been extensively studied to solve deadlock problems in Petri nets. However, most of the existing approaches based on elementary siphons can deal with the Petri nets in which all the transitions are supposed to be controllable and observable. This paper develops an elementary‐siphon‐based deadlock control policy for flexible manufacturing systems with uncontrollable and unobservable transitions. For elementary siphons, their complementary sets are successively expanded by considering unobservability and uncontrollability of transitions. Monitors are designed for the expanded complementary sets. The proposed method permits that there are arcs from monitors to a set of special uncontrollable transitions. Moreover, we show that the dependent siphons are always marked in the controlled system that is derived from the proposed method when there exist uncontrollable and unobservable transitions.