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The federal appeals court dismissed a challenge from the state of Nevada, local communities, the nuclear energy industry and environmental groups seeking to scuttle the plan.
But in a partial victory for opponents, the court also overturned a plan by the federal Environmental Protection Agency (EPA) to protect the public from radiation for 10,000 years, saying the government must protect against radiation leaks for a longer period, following recommendations of the National Academy of Sciences.
Environmentalists and Nevada leaders cheered the partial victory, saying it could kill the Yucca Mountain project.
"On one of the most crucial issues in the Yucca case, the court has sent EPA back to the drawing board to write a radiation protection standard that safeguards public health," said Geoff Fettus, attorney for the Natural Resources Defense Council who argued the case for the environmental groups.
"When dealing with a project of the magnitude of a nuclear waste repository, the law requires that EPA do it right rather than rush it through."
Under the best case, the nuclear storage site will not go into use until at least 2010. A workable waste storage site is deemed essential if nuclear power is to expand in the United States.
The Yucca Mountain waste repository is designed to house up to 70,000 tonnes of radioactive waste deep underground.
Energy Secretary Spencer Abraham said he was "pleased" with the ruling on the site selection.
As for the ruling on radiation standards, he said, his agency "will be working with the EPA and Congress to determine appropriate steps to address this issue."
The court ruled that the decision by the Department of Energy and the president leading to the selection of the Yucca Mountain site is "unreviewable."
But the court cited a National Academy of Sciences (NAS) report saying there was "no scientific basis for limiting the time period of the individual risk standard to 10,000 years or any other value."
"It would have been one thing had EPA taken the Academy's recommendations into account and then tailored a standard that accommodated the agency's policy concerns," the justices wrote. "But that is not what EPA did. Instead, it unabashedly rejected NAS's findings, and then went on to promulgate a dramatically different standard, one that the academy had expressly rejected."
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