An act to authorize appropriations for the Department of Energy for national security programs for fiscal year 1980, and for other purposes.

Department of Energy National Security and Military Applications of Nuclear Energy Authorization Act of 1980 - =Title I: National Security Programs= - Authorizes the appropriation of funds for fiscal year 1980 to the Department of Energy (DOE) for operating expenses incurred in carrying out national security programs for scientific research and development, strategic and critical materials necessary for common defense, and military applications of nuclear energy, including: (1) the defense inertial confinement fusion program; (2) the naval reactor development program; (3) weapons activities; (4) verification and control technology; (5) materials production; (6) defense waste management; and (7) the nuclear materials security and safeguards technology development program.

Authorizes funds for plant and capital equipment necessary for specific projects under the above programs.

=Title II: General Provisions= - Prohibits the use of funds authorized under this Act where the costs of the program exceed 105 percent of the program authorization or the costs exceed by more than $10,000,000 the amount authorized by this Act, whichever is the lesser. Prohibits the use of funds authorized by this Act for programs which have not been presented to, or requested of, Congress unless 30 calendar days have elapsed since the Secretary of Energy has presented to all the appropriate congressional committees a full and complete statement of the action proposed. Allows the written waiver of such requirement where such waiver is approved in writing by each appropriate committee of Congress.

Authorizes the Secretary to start any general plant project only if the maximum estimated cost of such project does not exceed $1,000,000. Stipulates that in the event any general plan project authorized by this Act has construction costs exceeding $1,000,000, the Secretary shall submit a complete report thereof to the appropriate congressional committees explaining the reasons for the cost variation. Prohibits the total amount of funds obligated to carry out all general plant projects authorized by this Act to exceed the total amount authorized to be appropriated for such projects by this Act.

Sets forth procedures for approval of projects that exceed the 25 percent estimated cost provision, and exempts from such procedures any project which has an estimated cost of less than $5,000,000.

Makes amounts appropriated pursuant to the authorization for management and support activities and for general plant projects available for use in connection with all national security programs of the Department of Energy.

Constrains total spending on a single advance plant engineering and design project to $2,000,000 unless the project is specifically authorized by law, and requires the Secretary to notify the appropriate congressional committees in the event the estimated cost of planning and design not specifically authorized by law exceeds $300,000.

Authorizes the Secretary to perform planning and design functions, utilizing available funds, for any Department of Energy defense activity construction project considered urgent for national defense needs or to protect property or human life.

Prohibits the use of funds authorized to be appropriated under this or any other Act for any purpose related to licensing of any DOE defense activity or facility by the Nuclear Regulatory Commission.

Prohibits the use of funds authorized to be appropriated by this or any other Act to pay any penalty, forfeiture, fine, or settlement resulting from noncompliance with the Clean Air Act where: (1) the Secretary finds that compliance is physically impossible within the statutory time limits; or (2) presidentially requested appropriations for compliance have not been made available by the Congress.

Expresses the sense of Congress that: (1) the Lawrence Livermore Laboratory; (2) the Sandia Laboratories; (3) the Los Alamos Scientific Laboratory are unique national assets which must remain dedicated to their primary defense focus aimed at maintaining United States preeminence in nuclear weapons systems technology; and (4) the long-standing contractual arrangements between the Federal Government and the University of California should continue as long as the national interest is being served.

Directs the Secretary to submit to Congress a plan, by February 1, 1980, to terminate contracts between the United States and the Regents of the University of California for work at the Ernesto Orlando Lawrence Livermore Laboratory and at the Los Alamos Scientific Laboratory. Requires the Secretary to study the types of contracts that would best provide for continuation of the work performed under such existing contracts. Directs the Secretary to include in any replacement contract terms to assure that: (1) the objectives and missions of such laboratory continue to be in the field of national security; (2) the transition be orderly and preserve employee rights and benefits; and (3) any new contractor may retain current management officials and employees to maintain and foster excellence in laboratory work.

Redesignates: (1) the Los Alamos Scientific Laboratory in New Mexico as the "Los Alamos National Scientific Laboratory;" (2) the Ernest Orlando Lawrence Livermore Laboratory in California as the "Ernest Orlando Lawrence Livermore National Laboratory;" and (3) the Sandia Laboratories in New Mexico and California as the "Sandia National Laboratories."

Authorizes the Waste Isolation Pilot Plant construction project in the Delaware Basin of New Mexico as a defense activity of the Department of Energy. States that such project is for the express purpose of providing a research and development facility to demonstrate the safe disposal of radioactive wastes resulting from defense activities. Directs the Secretary to consult and cooperate with officials of New Mexico in public health and safety matters with regard to such project.

Directs the Secretary to seek to enter into a written agreement with New Mexico outlining such State's responsibilities and authority with regard to such project.