Some experts, such as Robert Alvarez, a top Energy Department official during the Clinton administration, want the government to pick a new site for storing the waste. Alvarez recognizes the political difficulties ahead. “Everybody will just get angry if they learn their backyard might be a candidate site,” he says.

The Obama administration is considering whether to shift the management of nuclear weapons production to the Pentagon from the Energy Department, a step that would end more than 60 years of civilian control over nuclear bomb manufacture.

The goal would be to better focus the Energy Department on energy research, production and conservation, central priorities of the new administration.