The incidence of death by drowning greatly varies among different prefectures in Japan, mainly due to climate difference. However, there could be other factors affecting the incidence of deaths besides climate, for example, differences in regional death investigation systems. Here, we aimed to elucidate other such factors affecting the mortality data of drowning in the bathtub, especially the effects of discontinuing the medical examiner system. Police data in Kyoto and ambulatory care information in Yokohama were used. Data on cases of elderly individuals found dying or dead in the bathtub at home in winter 2014-2015 were obtained. The following data were collected for each case: age, gender, presence/absence of ambulatory transport, performance of autopsy, and cause of death. The autopsy and drowning rates in Kyoto were 0%, whereas both values in Yokohama were significantly higher at 93.1% and 89.4%, respectively (the denominator of each of the rates is the total number of elderly (aged 65 or over) individuals found dying or dead in the bathtub at home in each city during each winter). Despite no significant difference of incidence of total bath-related death, the proportion of drowning-related deaths was overwhelmingly higher in Yokohama than in Kyoto. The difference can be attributed to the difference in autopsy rates between the two cities, mainly caused by the presence/absence of a medical examiner system. Therefore, we should pay careful attention to future changes in autopsy/drowning rates in Yokohama, and ascertain whether the change might be continuously influenced by the abolishment of this system.