The Department, as the direct descendent of the Manhattan Engineer District, owns and manages the Federal properties at most of the major Manhattan Project sites, including Oak Ridge, Tennessee; Hanford, Washington; and Los Alamos, New Mexico. For over a decade, the Department, in cooperation with other Federal agencies, state and local governments, and other stakeholders, has pursued the possibility of including its most significant Manhattan Project properties within a Manhattan Project National Historical Park.

A panel of distinguished historic preservation experts convened in 2001 by the Advisory Council on Historic Preservation at the request of the Department of Energy recommended that the "ultimate goal" for the remaining major Manhattan Project properties, designated as Signature Facilities by the Department, "should be the formal establishment of these historic properties as a collective unit administered for preservation, commemoration, and public interpretation in cooperation with the National Park Service." In 2004, Congress passed the “Manhattan Project National Historical Park Study Act.” The Act directed the Secretary of the Interior, in consultation with the Secretary of Energy, to conduct a special resource study of the Oak Ridge, Los Alamos, and Hanford sites (and surrounding communities) "to assess the national significance, suitability, and feasibility of designating 1 or more sites within the study area as a unit of the National Park System."

In March 2006, the National Park Service (NPS) issued a notice of intent to prepare an Environmental Impact Statement, which would constitute the Special Resources Study. An NPS study team held public meetings at Oak Ridge, Hanford, and Los Alamos. By May 2007, the NPS study team, with full Department of Energy participation, had developed and assessed five alternatives. After much discussion, the NPS and the Department in early 2011 agreed to recommend the establishment of a park with three units at Hanford, Oak Ridge, and Los Alamos. The proposed three-site park would be managed as a partnership with the Department continuing to own and manage its properties and controlling access to them and the NPS providing overall management and interpretation and establishing visitor centers with a small number of rangers at each of the sites.

In July 2011, the Secretary of the Interior, with the Depart of Energy's concurrence, in a letter to Congress recommended the establishment of a three-site Manhattan Project National Historical Park. The Secretary recommended that the park be managed as a partnership between the park service and the Department of Energy. Congress currently is considering legislation. If a Manhattan Project park is authorized, the NPS would work with the Department and consult with the public and other stakeholders to develop a management plan.