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Flow shop production lines are very common in manufacturing systems such as car assemblies, manufacturing of electronic circuits, etc. In this paper. To model the uncertainty embedded in service times, all service times are first considered in the form of fuzzy numbers. Also, a systematic procedure is given for generating event-timing equations directly from the machine interconnections for a generalized flow shop system. Then, an adaptive fuzzy controller is proposed to adjust the number of parts per cycle entering the system. By the definition of a new measure for a production system the proposed fuzzy controller is implemented using only the time difference between outputs departure times and input release times. This approach is also robust to service time variations, and also to the system emergency conditions.