The Agency for Natural Resources, which was established in 1949, is the predecessor of the current Agency. In 1952, however, its duties were transferred to the Bureau of Mines, Bureau of Coal, Bureau of Mining Safety and the Bureau of Public Services, under the Ministry of International Trade and Industry.

The Ministry integrated the Bureau of Mines and Coal and the Bureau of Public Services in 1973 and the Agency for Natural Resources and Energy was established. As an external Bureau of the Ministry of Economy, Trade and Industry, which exclusively manages the administration of natural resources and energy, the Agency advances comprehensive policies in seeking to secure a stable and efficient supply of mineral resources and energy and to ensure the industrial stability of the country. Against the backdrop of the ever-increasing importance of natural resources and energy, the Agency is working on the improvement of its internal structure.

The reorganization of central government ministries and agencies in January 2001 integrated the administration of nuclear power safety, which had traditionally been managed by the Science and Technology Agency and the Agency for Natural Resources and Energy, and the administration of industrial safety, which had been managed by the Ministry of International Trade and Industry. Thus the Nuclear and Industrial Safety Agency was created as a special agency under the Agency for Natural Resources and Energy.