The present study was initiated to examine the activities of private clinic- or hospital-based occupational physicians (OPs) and to identify difficulties the OPs encountered in their occupational health service (OHS). A questionnaire was sent by mail to 557 OPs in Kyoto prefecture, Japan. Effective answers were obtained from 86 OPs who were private practitioners or physicians in hospitals and served as OPs on a part-time basis. Considering 3 h as a unit, a majority (92%) served <1 to 2 units/month. The leading fields of OHS provided by the OPs were general health examination and its follow-up, prevention of overwork, and mental health care, as well as support of workers on sick leave to return to work. OPs wished to allocate more time for maintenance and management of work and the work environment, mental health care, work area rounding, and attendance at the safety and health committee meetings. Difficulties were encountered most often in the management of mental ill health and overwork, and support of employees’ return to work. Many OPs also reported difficulties with industrial hygiene-related issues such as risk assessment, and maintenance and management of work and the work environment. The present survey identified difficulties that were frequently encountered by private clinic- and hospital-based OPs in their practice of OHS; these include issues on mental health, overwork and industrial hygiene. The needs to offering OPs specific opportunities to gain information and skills in these areas are stressed.