Japan now faces a serious physician shortage. After introducing the new postgraduate medical education (PGME) system and doctor-to-facility matching system, residents shifted their teaching hospitals from university hospitals to non-university hospitals. Because university hospitals had played a central role in allocating physicians to communities, the decrease in the number of physicians at university hospitals has driven this physician shortage. Japanese policymakers blame the new PGME for exacerbating this physician shortage and have tentatively agreed to reform the PGME to encourage residents to return to university hospitals. However, the PGME system should not be reformed only for political reasons; such a change requires a scientific basis. First, after the introduction of the new PGME, residents showed an improved clinical competence; therefore, it has accomplished its ultimate goal. Second, the residents’ satisfaction level in terms of the residency system and clinical skills training was significantly higher at non-university hospitals than at university hospitals. This implies that training conditions at university hospitals are not as good as at non-university hospitals, which explains the decrease in the number of physicians at university hospitals. Third, in 2009, the Japanese government increased the maximum medical school enrollment to mitigate the physician shortage. However, a simple increase does not solve the problem of physician shortage unless it also addresses the problem of physician maldistribution. Fourth, the number of females entering medicine is increasing, and women constituted 30% of newly certified physicians in 2010. In this era of physician shortage, female physicians are highly recommended as a human medical resource.