Abstract Background In Japan, medical error leading to patient death is often handled through the criminal rather than civil justice system. However, the number of cases handled through the criminal system and how this has changed in recent years has not previously been described. Our aim was to determine the trend in reports of patient death to the police and the trend in the resulting prosecution of healthcare providers for medical error leading to patient death from 1998 to 2008. Methods We collected data regarding the number of police reports of patient death made by physicians, next-of-kin, and other sources between 1998 and 2008. We also collected data regarding the number of resulting criminal prosecutions of healthcare providers between 1998 and 2008. Reporting and prosecution trends were analyzed using annual linear regression models. Results Reports: The number physician reports of patient deaths to the police increased significantly during the study period (slope 18.68, R2 = 0.78, P < 0.001) while reports made by next-of-kin and others did not. Mean annual reporting rates by group were physicians 130.1 (± 70.1), next-of-kin 29.3 (± 12.5), and others 10.4 (± 6.0). Prosecutions: The number of resulting criminal prosecutions increased significantly during the study period (slope 9.21, R2 = 0.83, P < 0.001). The mean annual prosecution rate was 61.0 (± 33.6). Conclusions The reporting of patient deaths to the police by physicians increased significantly from 1998 to 2008 while those made by next-of-kin and others did not. The resulting criminal prosecutions of healthcare providers increased significantly during the same time period. The reasons for these increases are unclear and should be the focus of future research.