Department of Energy Elimination and National Security Protection Act of 1999

(Sec. 105) Authorizes the Administrator to establish, consolidate, alter, or discontinue in the Energy Programs Resolution Agency any organizational entities that were entities of DOE. Sunsets the Agency three years after enactment of this Act. Directs the Comptroller General to report to Congress on the most efficient way to accomplish the complete abolishment of DOE and the transfer or termination of its functions.

Title II: Energy Laboratory Facilities - Establishes an independent Energy Laboratory Facilities Commission to reduce energy laboratories and programs through reconfiguration, privatization, and closure. Prescribes procedural guidelines.

(Sec. 205) Establishes the Energy Laboratory Facility Closure Account to fund implementation of such guidelines.

Title III: Privatization of Federal Power Marketing Administrations - Federal Power Asset Privatization Act of 1999 - Directs the Secretary of Energy to sell, at the highest possible price, all Federal electric power generation and transmission facilities supervised by, or coordinated with, the Federal Power Marketing Administrations (except the Bonneville Power Administration). Restricts such sales to domestic entities or U.S. citizens. Requires the Secretary to terminate Federal Power Marketing Administration operations upon completion of the sales. Directs the Secretary to retain a private sector firm through a competitive bidding process to serve as financial advisor with respect to such sales.

Expresses the sense of the Congress that the purchaser of any such facilities should offer to employ former Federal Power Marketing Administration personnel.

Mandates that sale proceeds be deposited into the Treasury.

Sets forth a sales completion deadline for each Power Marketing Administration concerned.

(Sec. 305) Mandates that the pertinent sales agreements require each purchaser providing electric power to customers within any region to insure that the price of electric power does not increase above the baseline price at a rate greater than ten percent annually.

(Sec. 306) Directs the Federal Energy Regulatory Commission (FERC) to issue to the purchaser of a hydroelectric generation facility a ten-year original license under the Federal Power Act to insure that the project will continue operations under the same conditions as were applicable prior to the sale. Grants FERC Federal Power Act jurisdiction over any such facility sold.

(Sec. 307) Amends the Energy and Water Development Appropriations Act of 1993 to repeal the prohibition against the use of appropriated funds for studies regarding a changeover from an "at cost" to a "market rate" or other noncost-based methodology for pricing hydroelectric power.

Title IV: Transfer and Disposal of Reserves - Transfers to the Secretary of the Interior all former DOE functions affecting the Strategic Petroleum Reserve. Instructs the Secretary to appoint an advisory board to monitor the sale of such reserves.

(Sec. 402) Transfers to the Administrator of the Energy Programs Resolution Agency all functions performed with respect to the naval petroleum reserves, except Naval Petroleum Reserve Numbered 1 (Elk Hills). Instructs the Administrator to: (1) obtain the highest possible price for the naval petroleum reserves; and (2) develop a joint plan with the Secretary of the Interior for disposal of the naval petroleum reserves within a specified timeframe.

Title V: National Security and Environmental Management Programs - Subtitle A: Defense Nuclear Programs Agency - Establishes the Defense Nuclear Programs Administration (the Administration) in the Department of Defense (DOD), headed by the Under Secretary for Defense Nuclear Programs, who shall be responsible for the exercise of all Administration powers and duties.

(Sec. 503) Transfers to the Under Secretary all: (1) DOD national security functions; (2) supervisory functions previously performed by DOE over Sandia, Los Alamos, and Lawrence Livermore National Laboratories; (3) functions of the Defense Threat Reduction Agency of DOD relating to nuclear weapons systems; and (4) functions of the Defense Nuclear Facilities Safety Board.

Authorizes the Secretary of Defense to transfer other nuclear weapons-related functions to the Under Secretary.

(Sec. 504) Restricts the transfer of funds by the Administration.

Subtitle B: Environmental Restoration Activities at Defense Nuclear Facilities - Amends the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 to require the Under Secretary to review ongoing and planned remediation activities consistent with this Act.

(Sec. 521) Sets forth guidelines for site-specific risk assessment, including a cost-benefit analysis of risk reduction, before the selection of a remedial action at a defense nuclear facility.

(Sec. 522) Instructs the Under Secretary to renegotiate the terms of any compliance agreement entered into with the Secretary of Energy, the Environmental Protection Agency, and the relevant State in order to have it reflect this Act.

Title VI: Disposition of Miscellaneous Particular Programs, Functions, and Agencies of Department - Directs the Energy Laboratory Facilities Commission to identify for the Congress all DOE research and development activities carried out at energy laboratories or institutions of higher education that perform a critical research function important to the long-term economic well-being of the United States.

(Sec. 601) Directs the Secretary of Energy to terminate the following DOE research and development activities: (1) clean coal technology; (2) fossil energy; (3) energy conservation; and (4) energy supply research and development (including basic energy sciences, magnetic fusion energy, solar and renewable energy, nuclear fission, and biological and environmental sciences).

Transfers from DOE to DOD specified weapons and defense activities.

(Sec. 602) Transfers to the Department of the Treasury all functions performed by the Energy Information Administration (EIA). Authorizes appropriations for the EIA.

(Sec. 603) Transfers to the Attorney General all functions performed by the Energy Regulatory Administration.

Title VII: Civilian Radioactive Waste Management - Amends the Nuclear Waste Policy Act of 1982 to terminate the Office of Civilian Radioactive Waste Management and to transfer its authority and assets regarding a repository for radioactive waste and spent nuclear fuel to the Army Corps of Engineers (the Corps). Requires: (1) the Corps to assume all obligations of the Office affecting the Yucca Mountain site; and (2) reissuance of Nevada State permits for the Corps. Prescribes procedural guidelines for Corps preparation and implementation of a Yucca Mountain site characterization plan.

(Sec. 702) Amends the Nuclear Waste Policy Act of 1982 to reaffirm that the obligation of the Secretary of Energy to accept high-level radioactive waste and spent nuclear fuel beginning by January 31, 1998, is absolute and is not dependent on commencement of operation of a repository or a monitored retrievable storage facility. States that such obligation shall be neither voided nor delayed for any reason.

Repeals: (1) the site selection limitation placed upon the siting of a monitored retrievable storage facility; and (2) the licensing conditions placed upon such facility.

(Sec. 703) Prescribes procedural guidelines for the licensing and expansion of an initial uranium storage facility.

Title VIII: Miscellaneous Provisions - Authorizes the Office of Management and Budget to make any determination regarding functions transferred under this Act and incidental transfers.