It is important to understand the chain of command when dealing with government organizations and at times it can get a little confusing. All of the military resale organizations and the morale, welfare and recreation activities fall under the executive branch of government. The three main agencies in the picture are the Defense Department (Commissaries, most Exchanges and most MWR), the Veterans Administration (Veterans Canteen Service) and the Department of Homeland Security (Coast Guard Exchanges and MWR). Some are principally funded by taxpayer dollars (Commissaries) and are referred to as appropriated fund activities and others are primarily self-funded and called nonappropriated fund activities.
The commissary program is managed by a Defense Agency through an operating board answering to the Undersecretary of Defense for Personnel and Readiness (USD P&R). The exchange and MWR programs report to their respective Services and ultimately through their Service Secretaries.
The overarching policy for the management of these activities is established by the President and administered by the Office of Management and Budget. The policy focal point for resale and nonappropriated fund activities resided in the office of the Director of resale and NAF policy in the office of the USD P&R.
The White House