The objective of this study is to develop a system that can automatically count the number of loaches ascending corrugated-pipe paddy field fishways by adopting the counting principle of resistivity fish counter originally designed for salmon. As the results of laboratory and in situ experiments, the counting mechanism of the resistivity fish counter could be applied to counting loaches by modifying the sensor allocation and adjusting voltage level. Counting precision was evaluated to be 86% with video monitoring analyses. In addition, long-term automatic operation in situ without permanent power sources was successful using rechargeable batteries (capacity 115Ah) and high-resolution and large-capacity data logger (memory capacity 2GB). The system could operate as long as 79 hours with two batteries connected in parallel.