Specifies the cooperative threat reduction (CTR) programs to be funded through O&M funds provided under this Act. Makes funds appropriated for such purposes available for three fiscal years. Allocates such funds among specified CTR programs. Prohibits such funds from being used for purposes other than those specified until 30 days after the Secretary reports to Congress on the new purposes. Provides limited authority to vary allocated amounts in the national interest, after congressional notification.

Directs the Secretary to seek to obtain all the permits required to complete each phase of construction of a project under CTR programs before obligating significant funds for such phase. Prohibits the obligation of more than 40 percent of the necessary funding for a new CTR construction project until the Secretary has obtained the necessary permits. Requires the Secretary to identify required permits for incomplete CTR construction projects, with the same 40 percent funding obligation limitation until all such permits are obtained. Authorizes the Secretary to waive the funding limitation in the national interest after notification of the defense and appropriations committees.

Prohibits CTR funds from being obligated for collaborative biodefense research or bioattack early warning and preparedness at a site in the former Soviet Union until the Secretary notifies Congress that: (1) no prohibited biological weapon research is being conducted at the site; and (2) appropriate security measures have been or will be put in place to prevent the theft of dangerous pathogens from the facility.

Requires the Secretary to appoint a U.S. Government employee as on-site manager before obligating any CTR funds for a project: (1) in a state of the former Soviet Union; (2) which involves dismantlement, destruction, or storage facilities, or the construction of a facility; and (3) with respect to which the total contribution by DOD is expected to exceed $50 million. Sets forth manager duties, including the identification and acquisition of necessary permits. Allows one individual to serve as on-site manager at more than one project, as long as the total of the projects at which the individual serves does not exceed $150 million for that fiscal year. Requires the Secretary, when directing an on-site manager to resume U.S. participation in such a project, to concurrently notify Congress.

Makes certain expenditure conditions required under the National Defense Authorization Act for Fiscal Year 2000 inapplicable to the FY 2004 obligation and expenditure of funds for the planning, design, or construction of a chemical weapons destruction facility in Russia if the President submits a certification to Congress that includes: (1) a justification for the national security waiver of such conditions; and (2) a plan to promote a full and accurate disclosure by Russia regarding the size, content, status, and location of its chemical weapons stockpile. Terminates such authority on September 30, 2004.

Requires the Secretary to make an annual certification to the defense and appropriations committees on the use of each facility for a CTR project or activity for which construction occurred during the preceding fiscal year.

Authorizes the President to obligate and expend current and prior year CTR funds for a proliferation threat reduction project or activity outside the states of the former Soviet Union if such project or activity will: (1) assist the United States in the resolution of a critical emerging proliferation threat; or (2) permit the United States to take advantage of opportunities to achieve long-standing nonproliferation goals. Requires that the project or activity be completed in a short period of time and that DOD be the entity most capable of carrying it out. Limits fiscal year obligation for such purpose to $50 million. Requires the President to notify Congress within ten days after exercising such authority.

Establishes the Veterans' Disability Benefits Commission to study, and report to the President and Congress on, the benefits provided to compensate and assist veterans and their survivors for disabilities and deaths attributable to military service. Terminates the Commission 60 days after its report. Directs the Secretary of Veterans Affairs to provide Commission funding.

Directs the Secretary to carry out a program to accelerate the research, development, and procurement of biomedical countermeasures, including therapeutics and vaccines, for protection of military personnel from attack by one or more biological, chemical, radiological, or nuclear (BCRN) agents. Authorizes the Secretary to enter into interagency or other Federal collaborative undertakings for such purpose. Requires coordination of program activities with similar activities of the Departments of Health and Human Services and Homeland Security. Authorizes the Secretary, in connection with the program, to: (1) acquire, lease, construct,or improve DOD laboratories and research facilities; (2) enter into personal services contracts; and (3) appoint highly qualified experts to carry out R&D under the program.

Requires the Secretary, on an ongoing basis, to: (1) assess current and emerging threats of the use of BCRN agents; (2) identify those agents that present a material risk of use against the armed forces; (3) assess possible health consequences of military personnel from such use; (4) identify those agents for which countermeasures are necessary; (5) assess the availability and appropriateness of such countermeasures; and (6) identify countermeasures which are appropriate for procurement for the DOD stockpile of biomedical countermeasures. Requires coordination of all such activities with the Secretaries of Homeland Security and Health and Human Services, allowing for the use of an interagency agreement. Provides funding from funds authorized under this Act.

Amends the Federal Food, Drug, and Cosmetic Act to permit the Secretary of Health and Human Services to authorize emergency use by the general public of certain drugs, devices, or biological products during the period of a declaration by the Secretary of Defense of a military emergency or potential military emergency involving a heightened risk to U.S. military forces of attack with a specified BCRN agent. Allows the Secretary of Health and Human Services to authorize the use of such drugs, devices, or products only after determining that: (1) a BCRN agent can cause a serious or life-threatening disease or condition; (2) the drug, device, or product may be effective in diagnosing, treating, or preventing such disease or condition; and (3) there is no adequate, approved, or otherwise available drug, device, or product for such use. Outlines related conditions on exercising such authority. Allows such authority until the earlier of the termination of the declaration of emergency or when emergency criteria or conditions are no longer being met. Directs the Secretary of Health and Human Services to promptly publish notification of the exercise of such authority. Authorizes the President to waive the right of military personnel to refuse the administration of such a drug, device, or product if the President determines that affording personnel such right is not feasible, is contrary to the best interests of the members affected, or is not in the interests of national security. Terminates the emergency authority if the President notifies Congress that the Project Bioshield Act of 2003, when enacted, provides an effective emergency use authority with respect to military personnel.

Amends the Immigration and Nationality Act to reduce from three years to one the required period of U.S. military service before eligibility for naturalization for U.S. citizenship. Prohibits a fee from being charged for the application, or for the issuance of a certificate of citizenship, under such circumstances (allowing no fee other than that portion which is paid to the State). Allows such citizenship to be revoked for separation from military service under other than honorable conditions, up until the time the person has served honorably for an aggregate five-year period.

Requires the Secretaries of Homeland Security, State, and Defense to ensure that naturalization applications, interviews, or other proceedings are available through U.S. embassies, consulates, and, as practicable, U.S. military installations overseas.

Directs the Secretary to prescribe a policy that facilitates the opportunity of a member of the armed forces to finalize naturalization for which the member has applied.

Provides such naturalization opportunities for members of the Selected Reserve of the Ready Reserve.

Provides that in the case of an alien spouse, child, or parent who was the spouse, child, or parent of a U.S. citizen at the time of the citizen's death and who (in the case of the spouse) was not legally separated, if the citizen served honorably in an active duty status and died as a result of an injury or disease incurred in or aggravated by such service, the alien spouse, child, or parent shall be considered an immediate relative and therefore eligible to benefits as a surviving spouse, child, or parent. Requires such alien to file for such benefits within two years of the citizen's death and only (in the case of the spouse) until the alien remarries. Outlines application requirements for adjustment of status (to naturalized citizens) for: (1) surviving alien spouses, children, and parents; and (2) spouses, children, and parents of lawful permanent resident aliens. Includes all persons granted such posthumous citizenship under this section as "U.S. citizens" or "citizen spouses" for purposes of the Immigration and Nationality Act. Makes this section effective with respect to persons granted citizenship due to deaths occurring on or after September 11, 2001.

Provides an expedited process for the granting of posthumous citizenship for members of the armed forces, with approval and documentation through the Director of the Bureau of Citizenship and Immigration Services.

Provides, with respect to the Navy, authorizations paralleling those provided for the Army under the previous title.

Terminates, or revises authorized amounts for, certain projects in FY 2002 and 2003.

Provides, with respect to the Air Force, authorizations paralleling those provided for the Army under title XXI.

Terminates an FY 2003 project at a classified location.

Authorizes the Secretary to acquire real property and carry out military construction projects in specified amounts at specified installations and locations. Authorizes the Secretary to carry out architectural and engineering services and construction design activities, improve existing military family housing units, and carry out certain energy conservation projects. Authorizes appropriations to DOD for fiscal years after 2003 for military construction, land acquisition, and military family housing functions of DOD. Limits the total cost of construction projects authorized by this title.

Terminates the authority to carry out certain FY 2003 projects.

Authorizes the Secretary to make contributions for the North Atlantic Treaty Organization (NATO) Security Investment Program and authorizes appropriations for fiscal years after 2003 for such Program.

Authorizes appropriations for fiscal years after 2003 for National Guard and reserve forces for acquisition, architectural and engineering services, and construction of facilities.

Terminates all authorizations contained in titles XXI through XXVI of this Act on October 1, 2006, or the date of enactment of an Act authorizing funds for military construction for FY 2006, whichever is later, with exceptions. Extends certain FY 2001 military construction projects.

Authorizes appropriations to the Department of Energy (DOE) for FY 2004 for: (1) activities of the National Nuclear Security Administration (NNSA) 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 nuclear waste disposal, and defense energy supply.

Amends the National Defense Authorization Act for Fiscal Year 2000 to repeal, after December 31, 2004, the requirement for annual updates of a long-term plan under the nuclear weapons stockpile life extension program.

States that groups of DOE officers and employees reviewing or advising on matters relating to DOE management and operating contracts shall not be considered advisory committees subject to the Federal Advisory Committee Act.

Directs the Secretary of Energy (Secretary, for purposes of this Division) to achieve and maintain a readiness posture of no more than 18 months for the resumption of U.S. underground nuclear tests.

Requires the Administrator for Nuclear Security to: (1) complete project selection for inclusion in the Facilities and Infrastructure Recapitalization Program of the NNSA no later than December 31, 2004; (2) terminate such Program no later than September 30, 2011; (3) report to the defense and appropriations committees conduct guidelines of the Readiness in Technical Base and Facilities program of the NNSA; and (4) continue the NNSA's Operations of Facilities program as a subprogram within the Readiness in Technical Base and Facilities program. Requires the Secretary to submit annually to the defense and appropriations committees a separate statement on the amounts requested for such fiscal year for the Operations of Facilities subprogram.

Amends the Spence Act to remove the F-canyon facility from DOE's authority to continue the processing, treatment, and disposition of legacy nuclear materials (leaving only the H-canyon facility). Revises a report requirement on the use of DOE funds for decommissioning the F-canyon facility.

Amends the National Defense Authorization Act for Fiscal Year 1994 to repeal the prohibition on R&D of low-yield nuclear weapons. Prohibits the Secretary from commencing the engineering development or any subsequent phase of a low-yield nuclear weapon unless specifically authorized by Congress. Requires a joint report from the Secretaries of State, Defense, and Energy to Congress assessing whether the repeal of such prohibition will affect the ability of the United States to achieve its nonproliferation objectives and whether changes in programs and activities would be required to achieve those objectives.

Prohibits the Secretary from commencing the engineering and development or any subsequent phase of a Robust Nuclear Earth Penetrator unless specifically authorized by Congress.

Directs the Administrator to report semiannually to the defense committees on the amounts available for the DOE defense nuclear nonproliferation programs.

Requires a spending plan report from the Administrator to the defense committees if, on September 30, 2004, the aggregate amount obligated but not expended for defense nuclear nonproliferation activities exceeds 20 percent of the amount already appropriated for such activities.

Directs the Secretary to study, and report to Congress on, purchasing weapons-grade uranium and plutonium from states of the former Soviet Union and safeguarding such purchases until they are rendered unusable for nuclear weapons.

Authorizes the President to obligate and expend international nuclear materials protection and cooperation program funds for a defense nuclear nonproliferation project or activity outside the states of the former Soviet Union if the President determines that such project or activity will: (1) assist the United States in the resolution of a critical emerging proliferation threat or permit the United States to achieve long-standing nonproliferation goals; and (2) will be completed in a short period of time. Requires DOE to be the entity most capable of carrying out such project or activity. Limits to $50 million the amount that may be so obligated in a fiscal year. Requires the President to notify Congress within ten days after any such obligation.

Directs the Secretary to appoint a Federal employee as an on-site manager before obligating any defense nuclear nonproliferation funds for a project in a state of the former Soviet Union that involves dismantlement, destruction, or storage facilities, and for which the total DOE contribution is expected to exceed $50 million. Describes manager duties, including the identification and acquisition of necessary permits. Requires the Secretary to notify Congress upon directing an on-site manager to resume U.S. participation in a suspended project.

Amends the Atomic Energy Act of 1954 to allow a majority of the members of the Nuclear Regulatory Commission to require that investigations of employees whose positions carry a high degree of importance or sensitivity be carried out by the Federal Bureau of Investigation (FBI) rather than the Civil Service Commission. Repeals a requirement that the FBI conduct investigations of employees assigned to a DOE Personnel Security and Assurance Program.

Directs the Secretary, beginning with FY 2005, to have in effect a policy for carrying out future defense environmental management matters of DOE. Requires a policy report from the Secretary to Congress.

Requires certain stockpile stewardship criteria information to be included by the Secretary in the 2005 stockpile stewardship plan submitted to Congress.

Requires a report from the: (1) National Institute for Occupational Safety and Health to Congress on the Institute's ability to obtain information necessary to carry out radiation dose reconstructions under the Energy Employees Occupational Illness Compensation Program Act of 2000; and (2) Secretary of Labor to Congress on the denial of claims under such Act.

Amends the Stump Act to require the inclusion in a required report of information on the integration and interoperability of R&D, procurement, and other activities undertaken by DOD and DOE during FY 2003 with respect to the Robust Nuclear Earth Penetrator.

Amends the Stump Act to add to it, for consolidation purposes, certain recurring and general provisions of law on DOE national security programs, including provisions under various defense authorization Acts, relating to: (1) atomic energy defense; (2) the naval nuclear propulsion program; (3) nuclear weapons stockpile stewardship and production; (4) tritium production; (5) nuclear proliferation; (6) defense environmental restoration and waste management; (7) the closure of defense nuclear facilities; (8) particular nuclear facilities, including the Hanford Reservation, Washington, and the Savannah River Site, South Carolina; (9) laboratories safeguards and security, including background investigations and polygraph programs; (10) classified information; (11) defense emergency response; (12) personnel matters; (13) employee education and training; (14) worker safety at nuclear weapons facilities; (15) budget and financial matters, including penalties under environmental laws; (16) administrative and other matters; (17) R&D; (18) facilities management; and (19) local impact assistance.

Authorizes appropriations for FY 2004 for the Defense Nuclear Facilities Safety Board.

Authorizes the National Defense Stockpile (NDS) Manager, during FY 2004, to obligate up to $69.701 million of the funds in the National Defense Stockpile Transaction Fund (Fund) for authorized Fund uses, including the disposal of hazardous materials that are environmentally sensitive. Authorizes the NDS Manager to obligate amounts in excess of such amount 45 days after notifying Congress that extraordinary or emergency conditions necessitate the additional obligations.

Amends the National Defense Authorization Act for Fiscal Year 2000 to increase the monetary objectives for receipts by the end of FY 2013 from the disposal of certain NDS materials.

Authorizes appropriations to the Secretary for FY 2004 to carry out activities relating to the naval petroleum reserves.

Maritime Security Act of 2003 -