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This work conducted a health impact assessment (HIA) of the Japanese Government's proposal concerning the introduction of so called "white-collar exemption" into the Japanese labor market. We adopted the Merseyside model and performed a rapid health impact assessment to assess the potential health effects of white-collar exemption. In this HIA, several health determinants which may possibly be affected, both positively and negatively, were identified based on experts' judgments. Literature evidence was assessed using PubMed and other databases. In addition, we searched for the opinions of those affected by white-collar exemption from internet web sites, and six concerns were identified. Long working hours were identified as the most serious concern by both experts and those affected. White-collar exemption may increase irregular working patterns which may be related to sleep disorder, stress, and cardiovascular disease. Family function and social participation will also be affected by irregular working patterns. On the other hand, in terms of stress, white-collar exemption may benefit from a higher degree of job control. There are possibilities that white-collar exemption may enable an improved work-life balance and enable access of some groups of the population, such as people with disabilities or parents looking after children, greater access to the labour market. However, it is uncertain whether the benefits of white-collar exemption would overcome those of the current free-time or flex-time systems. The present work provides a wide range of health impacts of white-collar exemption, and will hopefully attract the attentions of decision-makers and those likely to be affected in order to contribute to policy-making.