A federal judge in Atlanta has halted site preparation work at the controversial Clinch River breeder reactor project in Oak Ridge, Tenn., saying not even a tree may fall until all the necessary permits are granted.

The decision late Thursday by U.S. District Court Judge Marvin Shoob is the latest setback for the $3.2 billion project, whose backers thought as recently as three weeks ago that they had cleared their final hurdle after 12 years of debate.

Shoob ruled that the Department of Energy and the Environmental Protection Agency acted illegally Aug. 5 in giving the breeder a conditional waiver of EPA's permit requirements for water pollution control. No work can be done until a final environmental impact statement is completed and the permit is granted, the judge said.

His preliminary injunction, which came on a suit by the Natural Resources Defense Council and the Sierra Club, also in effect negates waivers of several permit rules granted Aug. 6 by the Nuclear Regulatory Commission.

Gordon L. Chipman, deputy assistant secretary of energy for nuclear reactor programs, said tree cutting had been scheduled to begin yesterday. "We're very disappointed," he said, indicating that an appeal is likely.

Chipman said the permit exemptions had been given only to allow preparation work to begin on the 271-acre site while normal licensing procedures continue. "The actual construction permit would not be granted until licensing is completed," he said. "No aspect of the licensing process would be circumvented."

Jacob Scherr of the NRDC disagreed. "DOE attempted to bend and break the rules in its desire to rush ahead with construction," he said. "We're gratified at the decision."

Critics of nuclear power have called the advanced plutonium- fueled power plant a "technological turkey" that is obsolete, unnecessary and even dangerous. President Carter tried to kill the project because it would "breed" more plutonium than it would use as fuel, and plutonium can be used in nuclear weapons.

But Congress overrode his objections by continuing to appropriate funds for the breeder. Last year, however, an effort to cut off the money supply failed by only two Senate votes and 20 votes in the House.

Defenders argue that the reactor's design has been updated and that the pilot project's construction is necessary to maintain U.S. energy security in an era when oil availability cannot be guaranteed.