The DFAA is a national administrative agency attached to the Defense Agency, and was founded on November 1, 1962 by the integration of the Procurement Agency and the Department of Construction of the Defense Agency.

Prior to that, defense facilities issues related to the USFJ had been managed by the Procurement Agency, and those related to the SDF had been handled by the Department of Construction of the Defense Agency respectively. The DFAA was established to exclusively implement defense facilities administration with efficiency.

The DFAA was given the status of Implementing Agency in the Central Government Reform of January 2001 whose responsibilities are principally related to the implementation of basic policies.