Organizational structure of the United States Department of Defense

The President of the United States is, according to the Constitution, the "Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States," now understood to also include the Air Force and other components of the DOD;^[2] and Chief Executive of the Federal Government. The Secretary of Defense is the "Principal Assistant to the President in all matters relating to the Department of Defense", and is vested with statutory authority (10 U.S.C. § 113) to lead the Department and all of its component agencies, including military command authority second only to the President.

The President and the Secretary of Defense exercise authority and control of the Armed Forces in two ways: operational, and administrative. Operational command (10 U.S.C. § 162) runs from the President, through the Secretary of Defense, to the Unified Combatant Commanders for missions and forces assigned to their commands. Administratively, authority runs from the President through the Secretary of Defense to the Secretaries of the Military Departments, i.e., the Secretary of the Army (10 U.S.C. § 7013), the Secretary of the Navy (10 U.S.C. § 8013), and the Secretary of the Air Force (10 U.S.C. § 9013). The Military Departments, organized separately within the Department, operate under the authority, direction, and control of the Secretary of that Military Department. The Secretaries of the Military Departments exercise authority through their respective Service Chiefs (i.e., Chief of Staff of the Army, Commandant of the Marine Corps, Chief of Naval Operations, Chief of Staff of the Air Force, and Chief of Space Operations) over forces not assigned to a Unified Combatant Command. Except as otherwise prescribed by law, the Service Chiefs perform their duties under the authority, direction, and control of the Secretaries of their respective Military Departments, to whom they are directly responsible.

In the Goldwater-Nichols Department of Defense Reorganization Act of 1986, Congress clarified the command line to the Unified Combatant Commanders and preserved civilian control of the military. The Act states that the operational chain of command runs from the President to the Secretary of Defense to the Unified Combatant Commanders. The Act permits the President to direct that communications pass through the Chairman of the Joint Chiefs of Staff from the Secretary of Defense and the Unified Combatant Commanders. This authority places the Chairman in the communications chain. Further, the Act gives the Secretary of Defense wide latitude to assign the Chairman oversight responsibilities for the Unified Combatant Commanders' activities.

Article II Section 2 of the Constitution designates the President as "Commander in Chief" of the Army, Navy and state militias.^[3] The President exercises this supreme command authority through the civilian Secretary of Defense, who by federal law is the head of the department, has authority direction, and control over the Department of Defense, and is the principal assistant to the President in all matters relating to the Department of Defense.^[4] The Secretary's principal deputy is the equally civilian Deputy Secretary of Defense who is delegated full powers to act for the Secretary of Defense. The Office of the Secretary of Defense (OSD) is the Secretary and Deputy Secretary's civilian staff, which includes several Under Secretaries and Assistant Secretaries of Defense with functional oversight responsibilities. The Secretaries of the Military Departments (i.e. Secretary of the Army, Secretary of the Navy, and Secretary of the Air Force) are subordinate to the Secretary of Defense. They have the authority under Title 10 of the United States Code to conduct all the affairs of their respective departments (Department of the Army, Department of the Navy, and Department of the Air Force) within which the military services are organized.^[5] Although subordinate to the Secretary of Defense, they are appointed by, and serve at the pleasure of, the President of the United States. As such, they cannot be removed from office by the Secretary of Defense, but can only be removed unilaterally by the President, or through impeachment by the Congress.

Historically, there have been challenges to civilian control. Most notably, during the Korean War, General Douglas MacArthur ignored civilian instructions regarding advancing troops toward the Yalu River, which triggered an introduction of massive forces from China. Also, on April 5, 1950, Representative Joseph William Martin Jr., the Minority Leader of the United States House of Representatives, released copies of a letter from MacArthur critical of President Harry S. Truman's limited-war strategy to the press and read it aloud on the floor of the house.^[6] President Truman relieved MacArthur of command, and MacArthur then explored political options against Truman.^[7] The Revolt of the Admirals is another example in the same era of a challenge to civilian control.

DoD policies and directives protect the policy of civilian control by establishing strict limitations on military members' political activities. For example, DoD Directive 1344.10 prohibits active-duty members of the military from running for office or making political appearances in uniform.^[8] However, enforcing this strict separation between the military and politics has been problematic. For example, over the years, many elected officials, including members of Congress, continued serving in the reserves while holding elected office. As another example, at a September 14, 2007, rally for Republican Presidential candidate John McCain in New Hampshire, seven on-duty uniformed Army personnel addressed the gathering.^[9] As another example, although DOD Directive 1344.10 prohibits political appearances by active-duty military members in uniform, Virginia Governor Bob McDonnell invited a uniformed Army Staff Sergeant to stand behind him during his televised Republican response to the 2010 State of the Union Address.^[10][11]