The positron ring and the electron ring of KEKB have their own dedicated movable masks to cut off spent electrons/positrons near the beam orbit to reduce background in the detector. The stepping motor drivers of the movable masks were controlled by a Programable Logic Controller (PLC), which was supervised by a VME-based IOC. The IOC and the PLC was connected with each other by using GP-IB interface for the communication. Recently, however, the GP-IB connection came to be unstable causing communication errors between the IOC and the PLC. In order to solve the problem, a new type of 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. In this control system, we replaced an existing ladder CPU with the IOC and the ladder program with an EPICS sequencer program for the efficiency of software development and ease of maintenance. The new IOC has been successfully serving since it was put in operation in September 2008. In this paper, we describe the details of the new control system and its experiences up to the date.