Due to the growing concerns over pollution issues during the high-growth period, such as the outbreaks of Minamata disease and Yokkaichi asthma, the need to unify the authority to regulate pollution issues, which had been dispersed across the various ministries and agencies, and to strongly advance measures against pollution became recognized. As a result, the Environmental Agency was established in 1971 as an external bureau of the Prime Minister's Office, for the purpose of taking charge of overall environmental issues, from pollution prevention to nature preservation.

However, as the subsequent development of economic society, problems of waste products became more serious, and global environmental issues began to arise such as the global warming and environmental pollution caused by a wide range of chemical substances, which the Ministry of the Environment has difficulty in fully responding under its traditional mandate.

Therefore, the recognition became heightened that a new ministry would have to take responsibility for the overall environmental administration including response to new issues, implement measures of its own volition, and take the initiative of environmental policies of the entire government. Following the reorganization of central government ministries and agencies in January 2001, environmental measures which were mandated by other ministries such as waste measures were unified, and the Ministry of the Environment was established as an independent ministry.