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Modern manufacturing systems are increasingly becoming highly dynamic due to the integration with advanced information technology in response to rapid changes in products and market conditions. A more flexible platform is critically needed for developing a new generation of manufacturing systems in order to address the challenges of uncertainty and flexibility requirements. This paper presents a mobile agent-based framework that supports dynamic deployment of control algorithms and tasks in automation systems. The framework is based on a mobile agent system called Mobile-C. It uses Ch, an embeddable interpretive C/C++ environment for mobile agent execution. Since Ch has been ported to most existing computing platforms, the framework can control automation systems that work in different operating systems. This mobile agent-based framework has been applied to the control of an automation work cell. Using an automaton package in Ch as a middleware, automation tasks can be described as high-level control programs and are portable to heterogeneous mechatronic devices that comprise the automation cell. The validation of the dynamic deployment of different tasks has been conducted in an experimental automation work cell that consists of a Puma 560, an IBM 7575, and a conveyor system. The results show that the mobile agent approach can effectively deploy and execute new control algorithms and tasks as mobile agents on any subsystem in a network.