Department of Energy National Security Act for Fiscal Year 2006

(Sec. 3113) Requires the Secretary to report to the defense committees on the management by the Secretaries of Energy, Defense, State, and Homeland Security of border security programs in countries of the former Soviet Union and other countries.

(Sec. 3114) Amends the Department of Defense Authorization Act, 1986 to include tribal organizations as participants under cooperative agreements to carry out emergency preparedness and response in connection with the disposal of lethal chemical agents and munitions.

(Sec. 3115) Makes the Savannah River National Laboratory a participating laboratory in the DOE laboratory directed research and development program.

(Sec. 3116) Makes amounts authorized under this section available to the Secretary to purchase essential mineral rights (the right to mine sand and gravel) at the Colorado DOE facility known as the Rocky Flats Environmental Technology Site. Outlines purchase conditions and limitations, including a release from any natural resource damage liability upon payment of a specified sum to environmental trustees for the facility. Revises management responsibilities and boundaries with respect to the Rocky Flats National Wildlife Refuge. Provides funding for the required trustee payment.

(Sec. 3117) Prohibits funds authorized to be appropriated to DOE under this Act from being made available for the Robust Nuclear Earth Penetrator.

(Sec. 3118) Expresses the sense of the Senate urging the Director of the National Institute for Occupational Safety and Health to: (1) provide to Congress interim reports of residual beryllium contamination at DOE facilities no later than 14 days after completing the internal review of such reports; and (2) publish in the Federal Register summaries of the findings of such reports.

(Sec. 3119) Requires a report from the Secretary to Congress on advanced technologies for nuclear power reactors in the United States.

Title XXXII: Defense Nuclear Facilities Safety Board - (Sec. 3201) Authorizes appropriations for FY2006 for the Defense Nuclear Facilities Safety Board.

Title XXXIII: National Defense Stockpile - (Sec. 3301) Amends the Strom Thurmond National Defense Authorization Act (NDAA) for Fiscal Year 1999 and the NDAA for Fiscal Year 2000 to revise required receipt objectives, for the end of FY2010 and FY2013, for previously-authorized disposals of excess and obsolete materials in the National Defense Stockpile (Stockpile).

(Sec. 3302) Authorizes the President to dispose of up to 8 million pounds of contained tungsten in the form of tungsten ores and concentrates from the Stockpile in FY2006. Allows such ores and concentrates to be sold to U.S. entities with ore conversion or tungsten carbide manufacturing or processing capabilities.

(Sec. 3303) Authorizes the Secretary of Defense: (1) to dispose of up to 75,000 tons of ferromanganese from the Stockpile during FY2006; and (2) if that disposal is completed before September 30, 2006, to dispose of an additional 25,000 tons before such date. Allows the additional disposal only if the Secretary certifies to the defense committees that it: (1) is in the interests of national defense; (2) will not cause undue disruption to the usual markets of ferromanganese producers and processors in the United States; and (3) is consistent with the requirements and purposes of the Stockpile.