This paper describes a supervisor system for monitoring the operation of automated agricultural vehicles. The system analyses all of the information provided by the sensors and subsystems on the vehicles in real time and notifies the user when a failure or potentially dangerous situation is detected. In some situations, it is even able to execute a neutralising protocol to remedy the failure. The system is based on a distributed and multi-level architecture that divides the supervision into different subsystems, allowing for better management of the detection and repair of failures. The proposed supervision system was developed to perform well in several scenarios, such as spraying canopy treatments against insects and diseases and selective weed treatments, by either spraying herbicide or burning pests with a mechanical-thermal actuator. Results are presented for selective weed treatment by the spraying of herbicide. The system successfully supervised the task; it detected failures such as service disruptions, incorrect working speeds, incorrect implement states, and potential collisions. Moreover, the system was able to prevent collisions between vehicles by taking action to avoid intersecting trajectories. The results show that the proposed system is a highly useful tool for managing fleets of autonomous vehicles. In particular, it can be used to manage agricultural vehicles during treatment operations.