Originally established as the 1030th USAF Auditor General group on 1 July 1948, the AFAA was redesignated a separate operating agency under the Comptroller of the Air Force on 31 December 1971 (DAF/PRM 516P, 20 Dec 71). Effective 24 July 1978, the AFAA was transferred under the Secretary of the Air Force with staff supervision from the Assistant Secretary of the Air Force (Financial Management) and direct access to the Chief of Staff (Secretary of the Air Force Order 502.1, 16 Oct 85)
The Goldwaters-Nichols DoD Reorganization Act of 1986 resulted in significant changes within the Secretariat and Air Staff. The change directly impacted AFAA operations by having the Auditor General of the Air Force (SAF/AG) report directly to the Secretary of the Air Force, with no oversight or supervision from other Secretariat offices (Secretary of the Air Force Order 502.1, 29 Oct 97). The Auditor General continues to have direct access to the Chief of Staff.