This paper focuses on the design and implementation of an execution controller of the navigation, guidance and control (NGC) tasks of remotely operated vehicles (ROV). A set of rules, guaranteeing the consistency and correctness of the control system, is defined on the basis of the topology, i.e. input-output relationships, of the execution level, and translated into constraints on a Petri net representing the NGC tasks as a discrete event system. A suitable Petri net search algorithm is defined for system reconfiguration. The proposed execution controller has been integrated in the Romeo ROV control system.