As the coronavirus pandemic continues to rage across the world, there is a greater need to improve the role and operation of public hospitals, which play an important role in the fight against the virus. A mail-in questionnaire survey of Japanese public hospitals was conducted to analyze the personal data protection challenges faced by medical institutions managed by local municipalities. Questionnaires were sent to 887 hospitals—with 20 or more beds—that are members of the Japan Municipal Hospital Association. This study summarizes and analyzes the unpublished portion of the 2016 survey conducted by Hashimoto and Moteki (2018), focusing on the characteristics of the municipal hospitals surveyed by their size and use of clinical indicators. Differences between large and small/medium hospitals regarding use of clinical indicators were found. Several small and medium-sized hospitals use a common consent form for the use of personal information, whereas larger hospitals use individual consent forms for different departments. The most used indicator was “average length of hospitalization and rate of hospital bed utilization” followed by “clinical path coverage rate” and “number of ambulances received and refused (rate).” There is a clear distinction in the clinical indicators measured in this study.