This work presents a new method for the synthesis of Petri net controller using the theory of regions. Control specifications are expressed as the conjunction of generalized mutual exclusion constraints (GMEC). The great advantage of the proposed method is to reduce the resolution difficulty of the theory of regions by introducing a concept of minimal cut in the reachability graph with minimal number of nodes. This new concept leads to minimize the total number of equations in the linear system of the theory of regions to synthesize the Petri net controller. To illustrate the present approach, an application is implemented on the Flexible Manufacturing System (FMS) at the ENIM (National School of Engineering of Metz), in FRANCE.