Final answer:
The Secretary of Defense has the primary and direct responsibility for SAPs within the DoD, overseeing the multiple branches of the U.S. armed forces and coordination with oversight bodies.
Step-by-step explanation:
The individual who has designated primary and direct responsibility for Special Access Programs (SAPs) within the Department of Defense (DoD) is the Secretary of Defense. This high-level civilian official oversees the entirety of the DoD, which includes various branches of the U.S. armed forces such as the Army, Navy, Marine Corps, and Air Force. Furthermore, the administrative staff works closely with entities like advisory committees and the inspector general's office to provide accounting and oversight, ensuring actions of the agency are appropriately managed. Although the DoD does not report directly to the President, it does provide reports to Congress for the necessary oversight and to secure funding.