Nuclear Waste Protection and Responsible Compensation Act - Prohibits commercial spent nuclear fuel and high-level radioactive waste (fuel and waste) from being transported offsite for away-from-reactor storage until a final license for a permanent disposition program is issued by the Nuclear Regulatory Commission.

Authorizes State and local governments to negotiate with nuclear reactor utilities (utilities) to provide additional protections above the current Federal minimum standards to ensure that citizens and local communities are adequately protected from fuel and waste.

Requires each utility, beginning in FY 2000, to retain the amount such utility would be required to pay into the Nuclear Waste Fund and deposit such amount into a nuclear waste escrow account. Requires such funds to be collected by the Secretary of Energy from each utility in September of 2004 and 2009, and deposited into such Fund. Requires interest collected on the escrow accounts to be deposited into a Utility On-site Compensation Fund, to be used for the on-site storage of fuel and waste that should have been accepted by the Secretary. Requires the Secretary to establish the Federal Shutdown Reactor Fund for reactor shutdowns. Requires a utility which has been shut down to establish a Utility Shutdown Reactor Fund for the costs of on-site storage of fuel and waste at the shut down reactor.

Adjusts the current priority for reactor fuel and waste to place first in such priority all fuel and waste at shut down nuclear reactors.

Provides that such fuel and waste shall be considered to be non-defense wastes under this Act.