A new electron beam extraction line has been constructed for the Accelerator Test Facility 2 (ATF2) project. While the power supplies of the quadrupole magnets and bending magnets of the beam line are mainly controlled by an EPICS/PLC-based system developed by SLAC, a new control subsystem was required to control power supplies of other miscellaneous magnets. Since the human resource to implement the control system was highly limited, it is preferable that we choose a front-end controller which enables us to develop and maintain the software in an efficient manner. In order to satisfy this requirement, a new type of Input / Output Controller (IOC), which runs Linux on a CPU module of FA-M3 PLC, has been adopted. The CPU functions with standard I/O modules of FA-M3 on the PLC-bus. We found that running EPICS sequencer programs on the new IOC makes the development and maintenance of the software efficient. This paper describes the details of the IOC and its experiences in the operation of ATF2, such as long term stability, flexibility in the modification of the software and so forth.