Acting on an appeal by the South Australia (SA) state government, the full Federal Court unanimously quashed the forced acquisition by federal authorities of land for the dump near the outback town of Woomera.
The three-judge panel ruled that there was no "urgent necessity for the acquisition" and rejected federal government arguments that it would be contrary to public interest for the purchase to be delayed.
The conservative government of Prime Minister John Howard chose the South Australian site for storing low-level nuclear waste over the objections of the Labor-controlled state government.
The site was to store low-level radioactive waste from industry and the country's sole nuclear reactor, a research facility located in Sydney, 1,400 kilometers (840 miles) away.
The government ordered the compulsory acquisition of the dump site last year when the South Australian state government announced it would seek to block the project.
State Environment Minister John Hill hailed Thursday's court ruling as "a major win for South Australia".
"The judges found unanimously that the commonwealth (federal government) had improperly used their urgency power to obtain this land," he said.
Federal Finance Minister Nick Minchin said the government would likely appeal against the court decision.
"We will take legal advice but I think we will look very seriously at appealing that judgment to the High Court," Minchin told ABC radio.
"This really is important to the nation, the safe storage of radioactive waste," he said.
The Australian Conservation Foundation welcomed the court decision as a victory for democracy and the environment.
"The court has shown here today that the federal government exceeded their powers in trying to override the will of the South Australian community and the will of the SA parliament," spokesman David Noonan said.
"They have failed in the land acquisition for this nuclear waste dump and they will not get away with imposing a nuclear waste future against SA's interests."
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