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For remote-controlled multi-recipe processes, certain issued commands may lead to undesired resource conflicts and deadlock states. Moreover, as a result of the communication delay and packet loss in the Internet, remote control of a group of certain steps are recommended rather than control of each step. For these Web-based control systems, this paper proposes a three-level architecture for hierarchical supervision. In the upper supervisory level, the supervisory agent guarantees that issued commands from the remote manager, in the middle command level, satisfy the resource sharing and deadlock-free requirements when executing a number of concurrent recipes, while the local controller, in the lower control level, performs the corresponding detailed operations to meet the requested tasks. In the present approach, Petri nets (PNs) are used to model, design, and verify the supervisory agent and local controller, and then, Java technology and ladder logic diagrams (LLDs) are adopted for implementation to achieve online supervision of the remote-controlled processes. To demonstrate the practicability of the developed supervisory approach, we apply it to a three-recipe flexible manufacturing system (FMS) controlled over the Internet.