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Agent-based software systems are becoming a key automation software technology for intelligent manufacturing systems. This paper presents an original approach to formalise the development process of agent-based supervisory control systems. A design-validation methodology is proposed, which focuses on the seamless integration of production system's development and agent-based intelligent automation system's development processes. It is based on the use of coloured Petri net as formal specification tool, and the results of its application to a cast study (an industrial installation) are investigated under functional, i.e., qualitative, and performance, i.e., quantitative, objectives.