Organotins (OTs) are globally ubiquitous contaminants. Contamination of OTs, particularly butyltins (BTs), has been suspected to cause immunosuppressive effects leading to subsequent infectious diseases or opportunistic infection by pathogens in marine mammals. In the present study, we collected individuals from five different populations of finless porpoises (Neophocaena phocaenoides) from coastal areas of Japan (Seto Inland Sea, Ise Bay, Omura Bay, and Pacific coast) and Hong Kong, and measured OT concentrations in their livers. In addition, infection status of lung nematodes and liver trematodes was also observed to analyze the relationship between OT contamination and parasitic infection in finless porpoises. Hepatic OT concentrations were highest in the Hong Kong population, while levels in the Japanese populations were equivalent to those of other cetaceans from different locations. OT levels in Japan have been decreasing in the past few decades, while OT contamination has shown little improvement in Hong Kong. Observation of parasite infection in Seto Inland Sea porpoises revealed that 16 and 11 out of 22 individuals were infected by lung nematodes and liver trematodes, respectively. Additionally, a significant association between BT levels and parasitic infection status of lung nematodes was detected. Thus, the present study suggests that BTs could be a factor affecting parasitic infection, especially the presence or severity of lung nematodes in finless porpoises. Since chemical exposure may alter the susceptibility of organisms to infectious diseases, the interaction of chemical contamination with infectious diseases needs to be investigated in greater depth to understand the risk of population decline due to these factors in marine mammals.