A little late, but should be in effect now:
On June 15, 2015, the Department of Defense will launch a pilot of a new Integrated Lodging Program that will assist the Department in determining the best approach for providing quality government (DoD) and commercial lodging with the goal of achieving reduced rates, better services, and greater safety and security for the traveler.
As of June 15, the Joint Travel Regulations will require both Uniformed Service members and civilians on temporary duty travel to stay at government (DoD) or preferred commercial lodging facilities at select pilot locations. Quality standards and cost savings are primary considerations, and are intrinsic to this effort to ensure "duty of care" for travelers. Lodging reservations MUST BE made through the Defense Travel System or with a Commercial Travel Office when the Defense Travel System is not available. If travelers choose to stay in other lodging when government (DoD) or preferred commercial properties are available, reimbursement will be limited. The Defense Travel System will facilitate booking of these preferred properties at the select pilot locations.
Additional information including frequently asked questions is available on the Defense Travel Management Office website at: http://www.defensetravel.dod.mil/site/lodging.cfm.
Changes are scheduled to appear in the JTR dated 1 July 2015.