When death is caused by a disease, the precise cause of the death must be determined to promote health and contribute to prevention efforts. The circumstances of death should also be clarified so that measures can be taken to prevent the recurrence. Statistics regarding the cause of death must be accurate, and such statistics are shaped by the determination of the cause of death. We examined the annual cause of death rankings and the mortality rate in Japan during the 25-year period 1993–2017. We identified improvements that are needed to provide more precision in the cause of death statistics, with a focus on variations in the rankings, and we describe the peculiar and vulnerable aspects of the Vital Statistics system in Japan; for example, at one time the national government advised physicians to not list “heart failure” as the terminal stage of a condition on a death certificate, and the “heart disease” mortality rate thus tended to decline in that period. The ranking of “heart disease” as a cause of death decreased, but its mortality rate subsequently increased again. In addition, the “pneumonia” mortality rate has remained high over the past few years, but it abruptly decreased in 2017, when “aspiration pneumonia” was separated as a cause from other pneumonias. The “senility” mortality rate has increased annually, and it is a leading cause of death. It is important that physicians understand the underlying causes of death and provide that without being influenced by the reporting customs of the times.