Nuclear Waste Policy Act of 1999 - Amends the Nuclear Waste Policy Act of 1982 to revise and rename it the Nuclear Waste Policy Act of 1999.

Instructs the Secretary of Energy (the Secretary) to: (1) develop and operate a repository for the permanent geologic disposal of spent nuclear fuel and high-level radioactive waste; (2) accept spent nuclear fuel and high-level radioactive waste by no later than June 30, 2003; (3) provide for the transportation of such wastes; (4) pursue expeditiously the development of each component of the integrated management system; and (5) engage private sector participation to the greatest extent possible in the implementation of this Act.

Shields the United States from any financial liability for the Secretary's failure to meet acceptance or emplacement deadlines under this Act.

Instructs the Secretary to utilize truck transport to move spent nuclear fuel and high-level radioactive waste from the mainline rail line at Caliente, Nevada, to the interim storage facility site. Authorizes the Secretary to use rail transportation to meet the requirements of this Act if direct rail access becomes available to the interim storage facility site. Sets a deadline for the Secretary to develop the capability to commence rail to truck intermodal transfer at Caliente, Nevada.

Provides for heavy-haul transportation route and truck transportation.

Requires the Nuclear Regulatory Commission (NRC) to enter into a Memorandum of Understanding with the City of Caliente and Lincoln County, Nevada, to provide advice to the Commission regarding intermodal transfer and to facilitate on-site representation. Provides that reasonable expenses of such representation shall be paid by the Secretary.

Prescribes procedural guidelines for the availability of safe transportation for spent nuclear fuel and high-level radioactive waste from Department of Energy sites and sites designated by the contract holders to mainline transportation facilities and from mainline transportation facilities to the interim storage facility or repository, using routes that minimize transportation through populated areas. Mandates development of a comprehensive management plan that ensures safe transportation of spent nuclear fuel and high-level radioactive waste from Department of Energy sites and sites designated by the contract holders to the interim storage facility site.

Prescribes guidelines under which the Secretary shall: (1) develop a transportation plan for the implementation of each shipping campaign from each site at which high-level nuclear waste is stored; and (2) evaluate the relative safety of proposed shipping routes and modes from each shipping origin to the interim storage facility or repository compared with the safety of alternative modes and routes.

Prescribes general transportation requirements, including technical assistance and funds for: (1) States, Indian tribes, and nonprofit employee and joint labor-management organizations for worker health and safety training and education programs; and (2) emergency response situations.

Prohibits shipments of spent nuclear fuel and high-level radioactive waste through any grant-eligible jurisdiction: (1) until the Secretary has determined that personnel in all State, local, and tribal jurisdictions on primary and alternative shipping routes have met acceptable standards of training for emergency responses to accidents involving spent nuclear fuel and high-level nuclear waste; and (2) unless technical assistance and funds to implement safe transportation procedures and emergency response situations have been available for at least three years prior to shipment.

Directs the Secretary to award grants to States and Indian tribes for development and implementation of plans to prepare for such shipments.

Requires a transporter of nuclear waste under contract with the Secretary to comply with all governmental and Indian tribal transportation regulations.

Instructs the Secretary of Transportation to promulgate employee protection training standards for workers directly involved in nuclear waste transportation, storage, and disposal.

Prescribes guidelines under which the Secretary of Energy is instructed to design, construct, and operate an interim storage facility for spent nuclear fuel and high-level radioactive waste in accordance with Federal licensing regulations governing independent spent fuel storage installations.

Prescribes guidelines under which the Secretary is instructed to implement site characterization activities at the Yucca Mountain site in accordance with the Secretary's program approach to site characterization (Civilian Radioactive Waste Management Program Plan).

Prescribes authorization guidelines for an interim storage facility, and for a permanent repository, including: (1) licensing standards; (2) compliance with the National Environmental Policy Act; and (3) land withdrawal.

Instructs the Secretary to offer Nye County, Nevada, an opportunity to designate an on-site oversight representative to conduct on-site oversight activities at the Yucca Mountain site. Authorizes the Secretary to: (1) make grants to enable affected Indian tribes or local governmental units to monitor and review the impact of the integrated management system upon residents at the Yucca Mountain site; and (2) offer financial and technical assistance, as well as payments in lieu of taxes, to help a tribe or local governmental unit to mitigate such impact.

Instructs the Secretary to offer to enter into separate benefits agreements with Lincoln and Nye Counties concerning the integrated management system.

Provides that acceptance of benefits under this Act by any affected Indian tribe or local government shall not be deemed an expression of consent to the siting of an interim storage facility or repository in Nevada.

Sets a deadline by which the Secretary of the Interior shall convey all Federal interest in specified property to Nye County, Lincoln County, or to the city of Caliente, Nevada.

Authorizes the Secretary to grant payments in lieu of taxes to any affected Indian or local jurisdiction until the termination of the integrated management system activities.

Prescribes contract guidelines for the Secretary to accept title to, and transport, store, and dispose of spent nuclear fuel or high-level radioactive waste. Prescribes a schedule of annual fees payable to the Secretary of Energy for electricity generated and sold by civilian nuclear power reactors, and of a one-time fee for spent nuclear fuel used in such generation. Requires the Nuclear Regulatory Commission to suspend the license of any licensee who fails or refuses to pay such fee. States that payment of the fee relieves the payer of further financial obligation to the Federal Government for its long-term storage or permanent disposal of spent fuel or waste derived from spent nuclear fuel used to generate electricity in a civilian power reactor before January 7, 1983.

Continues the Nuclear Waste Fund. Prohibits the Secretary from expending certain funds to design or construct packages for the transportation, storage, or disposal of spent nuclear fuel from civilian nuclear power reactors.

Establishes the Office of Civilian Radioactive Waste Management within the Department of Energy, whose Director shall be directly responsible to the Secretary for executing the Secretary's functions under this Act. Mandates audits of Office operations, including its contractors and subcontractors at all tiers, and audits of management practices and performances every five years.

Directs the Secretary to issue a final rule establishing the appropriate portion of the costs of managing high-level radioactive waste and spent nuclear fuel allocable to the interim storage or permanent disposal of high-level radioactive waste from atomic energy defense activities and spent nuclear fuel from foreign research reactors. Authorizes appropriations.

Preempts State and local law in favor of this Act. Precludes this Act from being construed as: (1) constituting either an express or implied Federal reservation of water rights for any purpose arising under it; (2) authorizing the Federal use of eminent domain to acquire water rights; or (3) limiting the exercise of water rights as provided under Nevada State laws.

Grants U.S. courts of appeals original and exclusive jurisdiction over civil actions under this Act. Prescribes guidelines for NRC licensing hearings regarding facility expansions and transshipments.

Prohibits the Secretary from conducting site-specific activities for a second repository unless the Congress has specifically authorized and appropriated funds for them.

Requires the NRC to promulgate regulatory guidelines for: (1) financial arrangements for low-level radioactive waste site closures; and (2) training and qualification of civilian nuclear powerplant personnel.

Delineates an emplacement schedule for contract holders' spent nuclear fuel and high-level radioactive waste.

Prohibits: (1) subseabed or ocean water disposal of spent nuclear fuel or high-level radioactive waste; and (2) any obligation of funds for any such related activity.

States that the Secretary's acceptance of spent nuclear fuel or high-level radioactive waste constitutes a transfer of title to the Secretary. Authorizes the Secretary to: (1) accept all spent nuclear fuel withdrawn from Dairyland Power Cooperative's La Crosse Reactor; and (2) pay for the on-site storage of such fuel until DOE removes it from the site.

Expresses the sense of the Congress that to the greatest extent practicable all equipment and products purchased with funds made available under this Act should be American-made. Requires each Federal agency to give notice of this policy to any entity to which it provides financial assistance or contracts. Prohibits contracts with persons falsely labeling products as "Made in America."

Continues the Nuclear Waste Technical Review Board. Authorizes appropriations.

Directs the Secretary to take necessary action to improve the management of the civilian radioactive waste management program to ensure to the maximum extent its operation like a private business.

Directs the Secretary to employ, on an on-going basis, integrated performance modeling regarding site characterization.

Instructs the Secretary to report to the Congress on actions planned to implement this Act, (including the development of the Integrated Waste Management System) and to provide annual status updates.

Provides for continuation of specified contracts executed under the Nuclear Waste Policy Act of 1982.