Integration amongst various decision-making processes, such as planning, design, and operation is necessary to dynamic and flexible batch production. To achieve a batch production integration, utilization of common models used for various decision-making processes is an effective approach. From this point of view, a batch system common model as described by a Petri net is proposed. In this article, a fault diagnosis technique for batch processes is presented using information about fault propagation and the possibilities of integration of fault analysis and controller synthesis are discussed on the basis of the Petri net based common models.