Allen was assigned in December 1961 to the Office of the Secretary of Defense, Space Technology Office, in the Directorate of Research and Engineering, Washington, D.C. From June 1965 to February 1973, he was assigned to the Office of the Secretary of the Air Force, initially in Los Angeles, California, as the Deputy Director for Advanced Plans in the Directorate of Special Projects. Allen next moved to The Pentagon in June 1968 as the Deputy Director of Space Systems, and in June 1969, he became the Director. He returned to Los Angeles in September 1970 as the assistant to the Director of Special Projects and in April 1971 became the Director of Special Projects, with additional duty as the Deputy Commander for Satellite Programs of the Space and Missile Systems Organization.