Developing FMS controllers has been a difficult problem largely because of the variety of the system configuration. The purpose of this paper is to develop a method of building an FMS controller. The controller consists of control module and execution module. A hierarchically layered structure of these modules is proposed. The control module generates abstract-level execution requested by identifying a set of activities that can be executed without creating any irregular state. The execution module transmits the requests to physical device controllers and reports back the completion of the requests to the control module. Both of these two modules use Petri Net-based models. In this paper, a controllable Petri Net model is automatically synthesized from declarative specifications provided by a user. An execution Petri Net model for the execution module is designed to ensure the consistency between the control module and the real target system. The controller operates in MMS on TCP/IP and UNIX environment.