A particular characteristic of a manufacturing system concerns the complexity and the presence of uncertainties along with the difficulties in building analytical models that capture the system in all its important aspects. Hence, simulation remains one of the most widely used tools to fill this need. The objective of this article is related to the potential improvement of computer simulation as applied to the control of manufacturing system by introducing a two-level fuzzy-logic based control structure. On the lower level of the hierarchy, there is an adaptive fuzzy controller for each specific production module which can automatically sythesize itself to regulate the flow of the material into a system, and in the upper level, a supervisor has the task of coordinating and tuning the local controllers by using the performance measurements characterizing the overall system's current behavior to achieve better performance and restrict the system in admissible domain.