To ensure the safety of medical equipment, appointing medical equipment safety managers (MESMs) in medical institutions was made compulsory in Japan in 2007. This study aimed to describe the current status of clinical engineers (CEs) and analyze changes in the specialties of those selected as MESMs in Japan. We analyzed 2008 and 2011 government census data on hospitals. The proportion of hospitals where CEs were MESMs increased significantly, from 16.6% in 2008 to 18.5% in 2011. Although CEs are optimal as MESMs in terms of expertise, only one-third of hospitals (2,743/8,157) employed CEs.