Introduction: The aim of this study was to investigate the current status of patient safety management systems in primary care clinics in Japan.Methods: An online survey on patient safety management systems was conducted among primary care physicians certified by the Japan Primary Care Association who serve as clinic managers.Results: A total of 183 physicians participated in the survey. We found that 53.0%, 73.2%, 38.8%, and 32.8% had developed medical safety guidelines, nosocomial infection control guidelines, drug safety guidelines, and medical device safety guidelines, respectively. Furthermore, 64.5% had fewer than 10 incident/accident reports in the past year, the most common of which were prescription errors, vaccine errors, falls, and needle sticks.Conclusion: The issues identified in this study serve as a basis for promoting the development of educational programs and the creation of evaluation and improvement tools aimed at enhancing patient safety in clinics.