Beam loss monitors are essential diagnostic devices for the operation of J-PARC Main Ring, which aims at the acceleration of the world-highest-power proton beams. The data acquisition system of the beam loss monitors is required to measure the time structure of the output signal integrated during the acceleration cycle. The repetition rate of the measurement in the duration needs to reach at a level of tens of Hertz with time jitters less than a few milliseconds. In addition, the measured data must be accessible by the EPICS-based control system, which manages the whole accelerator control. In order to satisfy the requirement, a new type of Input / Output Controller (IOC), which runs Linux on a CPU module of FA-M3 Programmable Logic Controller (PLC), has been adopted. To execute the data acquisition, the CPU module functions with high speed data acquisition modules of FA-M3 on the PLC-bus. We found that the IOC could meet the requirements and the development and maintenance of the software for the IOC was considerably efficient.