TLANTA, April 18 The Nuclear Regulatory Commission has expressed doubt about the Bush administration's $3.8 billion plan to convert nuclear warheads to power-plant fuel, raising questions about whether it will become the nation's principal method of disposing of plutonium once aimed at the Soviet Union.

The doubts expressed by the commission, which is independent, appear to bolster the contention of the State of South Carolina that plutonium scheduled to be shipped from Colorado next month may never be converted to fuel at a government plant on the Savannah River.

South Carolina's governor, Jim Hodges, has threatened to block the shipments with state troopers unless the federal government guarantees that the plutonium will be removed from the state if the conversion program collapses.

The conversion plan is part of the 1996 agreement between the United States and Russia to decommission most of their cold war missiles and render the plutonium inside unusable for weapons. In January, the Bush administration announced that it had settled on a plan to process the warheads into mixed-oxide fuel for power plants, but the plan is contingent upon the Russians doing the same.

Most of the converted fuel, known as MOX, would have gone to two nuclear power plants in North Carolina and South Carolina run by the Duke Energy Corporation. In February, Duke officials told the regulatory commission that the conversion plan might never happen.

"Substantial uncertainties and contingencies continue to surround the program," the company wrote in a legal memorandum. It said the program's future depended on Russia's cooperation, future decisions by the federal Department of Energy, and the ability of the department to get a license for the conversion plant.

At the time, Duke was fighting off a challenge by two environmental groups, which argued that the company's reactor licenses should not be renewed if Duke planned to use the untested MOX fuel. On April 12, the regulatory commission dismissed the environmental groups' challenge, saying the future of the MOX program was so uncertain that it should not be the basis of a license challenge.

The commission said "we see no reason to doubt Duke's statement" that the MOX program was riddled with uncertainties, and it said any number of events could occur in the next six years that would make it impossible to use the converted fuel in a power plant.

The statement was welcomed in the South Carolina governor's office, which said it had every right to worry that the plutonium would not be processed and would remain in the state permanently.

"The Duke and N.R.C. statements validate Governor Hodges's position against allowing plutonium into South Carolina without an ironclad agreement that it will be removed," said Cortney Owings, a spokeswoman for the governor. "There are a lot of questions that need to be answered involving this process."

The Department of Energy has said it must begin shipping plutonium from the Rocky Flats nuclear site outside Denver by May 15, or it will not make its deadline to close down the site by 2006.

Ambassador Linton Brooks, chief of the Energy Department's nuclear nonproliferation programs, said today that the regulatory commission's position simply stated the obvious fact that the program was not finished yet. But Mr. Brooks said resolving the dispute with South Carolina would eliminate much of that uncertainty.

"There are a lot of things that we need to make sure come out right, and that's why we're so anxious that we resolve the issue with the state," he said. "The biggest impediment to getting the Russian program going is uncertainty about our program."

The department's insistence that the shipments begin quickly was supported on Wednesday by the Kaiser-Hill Company, a private contractor that is cleaning up the Rocky Flats site for the department. In November, the president of the company said it did not matter when the first shipments began, but in Wednesday's statement, the company agreed with the department that the shipments must begin by late spring or the deadline would not be met.

Company officials said they had a strict timetable that required the plutonium to be removed by 2003, so full decontamination of the site could begin. The shipments from Colorado to South Carolina are estimated to take at least a year, assuming Governor Hodges allows the trucks in.

Senator Wayne Allard of Colorado, who has led the effort to close Rocky Flats, said the administration's support of immediate shipments from his state had nothing to do with his re-election campaign, as South Carolina officials have charged, but with the need to ensure that the agreement with Russia was proceeding.

"This issue has never been about Colorado vs. South Carolina," Mr. Allard said. "It has always been about national security."

If the shipments do not begin in 30 days, he said, "our national security and environmental safety will be compromised."