The federal government has begun polygraphing an estimated 5,000 nuclear weapons scientists and other sensitive employees at the Department of Energy, extending wholesale use of "lie detector" tests for the first time outside the CIA and National Security Agency.

Energy Secretary Bill Richardson ordered the testing in response to allegations that Chinese spies stole nuclear secrets from national laboratories run by the Department of Energy. But strong opposition is emerging as the DOE prepares to publish regulations this week spelling out how the polygraphs will be administered to thousands of contract workers and employees as a condition of employment in sensitive weapons programs.

"I expect continued concern and opposition from some of the laboratories and lab employees and civil liberties groups, and I fully expect lawsuits," Richardson said in an interview Friday.

The University of California, which runs the Los Alamos and Lawrence E. Livermore national laboratories under contract with the DOE, is the direct employer of many of the nation's nuclear weapons scientists. It said in a letter to Richardson last fall that it would object to using polygraph testing "broadly as a managerial tool" rather than "in a limited and more focused manner to investigate serious espionage situations."

Citizens for Los Alamos National Laboratory Employee Rights, a nonprofit group representing more than 60 Los Alamos employees, also considers polygraphs to be a "violation of employee rights" and plans to voice its objections at a joint hearing of the New Mexico and California legislatures next month, said Chris Mechels, the organization's vice president. John W. Shaner, a nuclear weapons physicist at Los Alamos's experimental explosives division, said last week that debate over polygraphs rages at the fabled home of the atom bomb north of Albuquerque.

"There's a huge number of people here who will say, 'Great, if that will solve the problem, let's get on with it,' " Shaner said. "But in discussions here there have been expressions of concern that bright young students coming out of school will look around and say, 'I can go and work at a university and not have to put up with this invasion of privacy--why should I go to Los Alamos?' "

Both Shaner and Houston T. Hawkins, Los Alamos's director of nonproliferation and international security, also said they were concerned about the scientific reliability of polygraphs.

Convicted spies like Aldrich Ames have fooled polygraphs, and numerous studies have shown the devices' tendency to register frequent "false positives," in which a quickened pulse rate is assumed to indicate that a subject is being deceptive even when that person is telling the truth.

Noting that studies also have found that the incidence of false positives increases with IQ, Hawkins said he worries that hundreds of careers could be ruined in a hunt for spies who may not exist. "Is that acceptable?" he asked.

Richardson approved the polygraphing as one of his first acts as energy secretary last fall, despite objections from some of his undersecretaries. At that time, however, it was not yet clear that the tests would be given across the board to large numbers of scientists, administrators and security officials.

Richardson said that he, too, is concerned that the tests could hurt the Energy Department's ability to recruit first-rate scientists. But, he said, he decided it was important to join the CIA and NSA as the only federal agencies with widespread polygraph programs to send a message that protecting nuclear secrets is a top priority.

Edward J. Curran, a veteran FBI counterintelligence official who heads the DOE's newly created Office of Counterintelligence, said the first DOE employees to be polygraphed under the new program--and the only ones examined so far--are 57 of the 60 members of his own staff. Curran said it could take experts at the DOE's polygraph unit in Albuquerque four years to complete an initial round of examinations for the thousands of federal employees and private contractors working with highly classified nuclear secrets or safeguarding nuclear materials. Once the initial round of testing is completed, those workers will be subject to retests every five years, like employees at the CIA and NSA.

A draft copy of the regulations to be published in the Federal Register this week states that polygraphs will be used only to "address the narrow questions of whether the individual has engaged or is engaging in espionage, sabotage, terrorism, unauthorized disclosures of classified information, and unauthorized foreign contacts," not so-called "lifestyle" questions about prior drug use and extramarital affairs. The regulations also state that the polygraphs will be voluntary "because DOE cannot force an individual to take such an examination."

But those who refuse, Curran said, will be transferred out of sensitive nuclear programs that require access to highly classified information.

"To work in these sensitive programs, we set the standards," Curran said. "The employees don't set the standards."

Jeffrey H. Smith, an attorney and former CIA general counsel who has studied the use of polygraphs as a counterintelligence tool, said the DOE's program "raises very serious questions."

"They're going to have to have very careful procedures in place to protect the rights of the employees," Smith said. "And they're going to have to be careful that they don't over-rely on the polygraph. If the only indication of wrongdoing is 'deception' on the polygraph, they have to very quickly deal with that, so they don't harm the employee. This is a real challenge for them--to do it in a way that's fair to employees and protects the national security."

CAPTION: BILL RICHARDSON . . . fully expects lawsuits

CAPTION: EDWARD J. CURRAN . . . polygraphs will take four years