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The Air Force Manpower Analysis Agency was originally established in 1975 as the Air Force Management Engineering Agency, a separate operating agency reporting directly to Headquarters U.S. Air Force, when the Air Force decided it needed an agency to provide technical guidance and central direction to its management engineering program. In 1978, the Agency became a named unit and was realigned under the Air Force Manpower and Personnel Center. In 1985, it was re-designated as a separate operating agency under its original name under Headquarters U.S. Air Force. In 1995, the Air Force Chief of Staff directed the Air Force to "operationalize" its Total Quality Management Program. As a result, the agency merged with the Air Force Center for Quality and Innovation to become the Air Force Center for Quality and Management Innovation in 1996. To further operationalize quality, the manpower-quality function under the Air Force planning and programming guidance was re-engineered to streamline operations. As a result of that effort, the Agency was re-designated as the Air Force Manpower and Innovation Agency in 2001.
Starting in 1992, the Agency took over the field management engineering teams originally assigned to the Air Force Major Commands and reorganized them on a functional basis. The Agency was again re-designated as the Air Force Manpower Agency in 2004 and the teams were restructured into five numbered squadrons and two numbered flights to provide geographic and functional expertise, representing a shift in mission priorities to better support the expeditionary Air Force.
In 2012, the Agency was realigned under the Air Force Personnel Center as the Directorate of Manpower and later reactivated in its current form as the Air Force Manpower Analysis Agency in 2015. Its mission throughout its existence has been to provide U.S. Air Force leaders the analysis and tools to identify manpower requirements for the most effective and efficient accomplishment of Air Force missions.