Department of Energy National Security Act for Fiscal Year 2003 - Title XXXI(sic): Department of Energy National Security Programs - Subtitle A: National Security Programs Authorizations - Authorizes appropriations to the Department of Energy (DOE) for FY 2003 for: (1) activities of the National Nuclear Security Administration in carrying out programs necessary for national security, with specified allocations for weapons activities, defense nuclear nonproliferation activities, naval reactors, and the Office of the Administrator for Nuclear Security; and (2) environmental restoration and waste management activities in carrying out national security programs, with specified allocations for defense environmental management, other defense activities, defense environmental management privatization, and defense nuclear waste disposal.Subtitle B: Recurring General Provisions - Prohibits the use of funds appropriated pursuant to this subtitle for: (1) the cost of a program exceeding 115 percent of, or $5 million more than, the amount authorized; or (2) programs which have not been presented to, or requested of, Congress until the Secretary of Energy (Secretary) transmits to the defense and appropriations committees a full statement of the action proposed and 30 days have since expired.(Sec. 3122) Authorizes the Secretary to carry out minor construction projects using operation and maintenance funds or facilities infrastructure funds authorized by this title.(Sec. 3123) Places certain funding limits for general plant and construction projects of DOE. Requires congressional reports when amounts exceed such limits.(Sec. 3124) Authorizes the Secretary to transfer DOE-authorized funds: (1) to other Federal agencies for the performance of work for which such funds were authorized; or (2) between authorizations within DOE, to be merged with and available for the same purposes. Requires notification to the defense committees of any such transfers.(Sec. 3125) Directs the Secretary, before submitting a funding request for a construction project in support of a DOE national security program, to complete a conceptual design for such project. Requires a separate funding request for designs for which the estimated cost exceeds $3 million. Authorizes the Secretary to carry out construction design services in connection with any proposed construction project if the total estimated cost for the design does not exceed $600,000. Requires specific authorization by law for designs exceeding such amount.(Sec. 3126) Authorizes the use of DOE funds for planning, design, or construction activities for any DOE national security program that must proceed expeditiously in order to protect public health and safety, meet the needs of national defense, or protect property. Requires the Secretary to report to the defense and appropriations committees when funds are so used.(Sec. 3129) Directs the Secretary, during FY 2003, to empower each DOE field office manager with the authority to transfer defense environmental management funds from a program or project under such office's jurisdiction to another program or project in order to address a risk to health, safety, or the environment or to assure the most efficient use of such funds at that field office. Limits any such transfer to $5 million. Directs the Secretary to notify Congress within 30 days after any such transfer.(Sec. 3130) Directs the Secretary, during FY 2003, to empower each DOE field office manager with the authority to transfer weapons activities funds from a program or project of that office to another such program or project when such transfer is necessary to address a risk to health, safety, or the environment or will result in cost savings and efficiencies. Limits any such transfer to $5 million. Directs the Secretary to notify Congress within 30 days after any such transfer.Subtitle C: Program Authorizations, Restrictions, and Limitations - Prohibits funds authorized to DOE under this Act for environmental management cleanup reform activities from being obligated or expended until the Secretary publishes in the Federal Register, and submits to the defense and appropriations committees, a report setting forth project selection and priority criteria, or notifies such committees that such criteria will not be established. Outlines provisions for funding availability if such criteria are not established.(Sec. 3132) Directs the Secretary of Defense to report to the defense and appropriations committees on the Robust Nuclear Earth Penetrator.(Sec. 3133) Makes DOE funds authorized for the National Nuclear Security Administration available to the Deputy Administrator for Nuclear Security for Defense Programs for the development and implementation before the end of FY 2003 of a database for all national security laboratories to track the notification and resolution phases of Significant Finding Investigations.(Sec. 3134) Requires that, in any fiscal year after 2002 in which the Secretary plans to carry out activities relating to the development of a new or modified nuclear weapon, the Secretary shall specifically request funds for such activities in the budget submitted for that fiscal year. Provides exceptions: (1) for the nuclear weapons life extension program; (2) to modify an existing nuclear weapon solely to address safety or reliability concerns; or (3) to address proliferation concerns.(Sec. 3135) Amends the Department of Energy Organization Act to prohibit DOE amounts for national security programs and activities or activities under the Atomic Energy Act of 1954 from being obligated or expended unless funds therefor have been specifically authorized by law.(Sec. 3136) Prohibits the obligation or expenditure of more than $100 million of the amounts authorized for the elimination of weapons grade plutonium production until 30 days after the Administrator for Nuclear Security submits to the defense and appropriations committees a copy of a United States-Russian Federation agreement to shut down the three plutonium-producing reactors in Russia.Subtitle D: Proliferation Matters - Transfers from the Department of Defense to DOE the program to eliminate weapons grade plutonium production in Russia. Transfers associated funds, making such funds available for related DOE purposes.(Sec. 3152) Expresses the sense of Congress that the Secretary should develop a comprehensive program of activities to encourage all countries with nuclear materials to adhere to, or adopt standards equivalent to, the International Atomic Energy Agency standard on the Physical Protection of Nuclear Material and Nuclear Facilities. Directs the Secretary to require the Office of International Materials Protection, Control, and Accounting of DOE to conduct a study of the feasibility and advisability of developing a program to secure radiological materials outside the United States that pose a threat to U.S. national security. Requires the Secretary to report to Congress on: (1) such study's results; and (2) results of a study by the Secretary of the feasibility and advisability of various actions to reduce the risks associated with terrorist attacks on nuclear power plants outside the United States. Expresses the sense of Congress that the President should encourage amendment of the Convention on the Physical Protection of Nuclear Materials to make it: (1) apply to both domestic and international use and transport of nuclear materials; (2) incorporate fundamental practices for the physical protection of such materials; and (3) address protection against sabotage involving nuclear materials.(Sec. 3153) Amends the National Defense Authorization Act for Fiscal Year 1996 to repeal required reports on the obligation of funds for programs on fissile materials in Russia.(Sec. 3154) Amends the Spence Act to include within required reports on the status of nuclear materials protection, control, and accounting programs information on all countries having such materials (currently only Russia).Subtitle E: Other Matters - Amends the Atomic Energy Act of 1954 to extend until August 1, 2012, a program under which the Secretary indemnifies DOE contractors who perform activities that involve the risk of public liability and are not subject to financial protection requirements of such Act.(Sec. 3162) Amends the above Act to provide new requirements for worker health and safety rules for DOE nuclear facilities. Provides civil penalties against persons who have entered into an indemnification agreement that violates rules or regulations relating to industrial or construction health and safety and a specified DOE Order. Requires such regulations to take effect within one year of promulgation, authorizing the Secretary to provide for regulation variances or exemptions to the extent necessary to avoid serious impairment of U.S. national security interests. Provides enforcement guidance with respect to structures to be disposed of due to industrial or construction health and safety requirements. Requires the Secretary to include in each DOE contract a provision that allows an appropriate reduction in contract fees or costs in the event of a contractor violation of DOE health or safety regulations or orders.(Sec. 3163) Amends the National Defense Authorization Act for Fiscal Year 2000 to extend until January 1, 2005, the authority of DOE to pay voluntary separation incentive payments.(Sec. 3164) Makes funds authorized under this title available for FY 2003 payments to the Los Alamos National Laboratory Foundation for the support of public education needs of children in the vicinity of the Los Alamos National Laboratory, New Mexico.Subtitle F: Disposition of Weapons-Usable Plutonium at Savannah River, South Carolina - Directs the Secretary to submit to Congress a plan for the construction and operation at the Savannah River Site, South Carolina, of a mixed-oxide fuel facility for converting weapons-grade plutonium to a mixed-oxide fuel for use in commercial nuclear power reactors. Provides a construction schedule and production deadline dates, with the goal of achieving facility construction by January 1, 2009, and of processing 34 metric tons of plutonium into mixed-oxide fuel by January 1, 2019. Requires: (1) the Secretary to submit corrective action plans if the schedule and deadlines are not met; (2) the removal or disposal of unprocessed plutonium from the Site if the schedule and deadlines are not met; and (3) payments to South Carolina of economic and impact assistance associated with not meeting such schedule and deadlines. Directs the Secretary to submit to Congress: (1) a plan to address the failure to complete the planned removal or disposal; and (2) a report on the removal of the facility upon completion of operations.Requires the Defense Nuclear Facilities Safety Board to study and report to Congress and the Secretary on the adequacy of the K-Area Materials Storage Facility and related facilities at the Savannah River Site for the storage of defense plutonium and related materials in connection with the plutonium disposition program.Title XXXII: Defense Nuclear Facilities Safety Board - Authorizes appropriations for FY 2003 for the: (1) Defense Nuclear Facilities Safety Board; and (2) Department of the Army for the formerly used sites remedial action program of the Corps of Engineers.