The Ministry of Health, Labour and Welfare was newly established by the integration of the Ministry of Health and Welfare and the Ministry of Labour in January 2001 when the central government ministries and agencies were reorganized. As a result of the integration, the Ministry can comprehensively promote social security policy and labor policy.

In 1938, the Ministry of Health and Welfare integrated the work of the Public Health Bureau and Social Affairs Bureau of the Ministry of the Interior and the Postal Life Insurance Bureau of the Ministry of Communications. The Ministry of Health and Welfare was established as an agency to improve health of the people and enhance social welfare.

The Ministry of Labour was established in 1947 by separating the labor administration department of the Ministry of Health and Welfare. The Ministry was responsible for the employment and welfare of workers, working environment and vocational training. Furthermore, waste administration, which had been under the jurisdiction of the Ministry of Health and Welfare until then, was transferred to the Ministry of the Environment when the central government ministries and agencies were reorganized in 2001.