Finless porpoises Neophocaena spp. are under pressure from various anthropogenic impacts due to their coastal habitat. Net fishery bycatch is considered a major risk for the populations around Japan, and mitigation measures are required. We carried out a long-term study to assess the efficiency of acoustic pingers in reducing the encounter rates of narrow-ridged finless porpoises with fishing nets. We used a passive ultrasonic event recorder (A-tag) to obtain acoustic encounter rates of echolocating finless porpoises and compared results for the presence and absence of pinger transmissions in Omura Bay, Japan, over two 8-mo periods (2011 and 2012). Encounter rates were significantly lower during periods when pingers were in operation, but the effect of pingers decreased with time. By the eighth month of the study in each study year, the number of encounters during the ensonified period was greater than that during periods without pingers, suggesting habituation. When pingers were reactivated at the study site after 4 mo of silence, the encounters with the active pingers returned to the lower level observed at the beginning of the experiment. These results reveal that the pingers effectively induce avoidance in porpoises, but that this effectiveness only lasts for a few months, which is likely due to habituation which could be mitigated by alternating periods of several months of silence between periods of active pinger use.