In 1950, the National Police Reserve was established to supplement the National and Regional Police and the municipal police forces. In order to develop a defense mechanism suited to an autonomous and independent defense system, the National Police Reserve and the Maritime Guard were amalgamated to form the predecessor of the Agency, the National Safety Agency.

The National Safety Agency became the Defense Agency in 1954, and has since protected the peace and independence of Japan, carrying out its duties of managing and administering the Ground, Maritime and Air Self-Defense Forces, as well as the work related to these duties.

At the time of its establishment, the Internal Bureau consisted of the Secretariat of the Minister of State for Defense, the Bureau of Defense Policy, the Bureau of Education, the Bureau of Personnel, the Bureau of Accounting and the Bureau of Equipment. However, since its re-establishment in the reorganization of central government ministries and agencies as an external bureau of the Cabinet Office, it is constituted by the Secretariat of the Minister of State for Defense, the Bureau of Defense Policy, the Bureau of Defense Operations, the Bureau of Personnel and Education and the Bureau of Finance and Equipment.