WASHINGTON -- For nearly three years, Energy Department officials could have accessed the unsecured personal computer of a suspected nuclear spy and discovered a mountain of classified nuclear weapons data stored in it.

They declined to do so, even though such spot checks of federally owned computers have been routine in the past. Energy Department and federal agents believed that once FBI agents began investigating a former scientist at the Los Alamos National Laboratory, N.M., he came under the protection of a federal computer privacy law designed to shield citizens from intrusive law enforcement agents.

Energy Department officials acknowledged this week that the scientist, Wen Ho Lee, transferred huge amounts of classified nuclear weapons design data to an unsecured computer that could have been accessed by the outside world.

Days after he failed an FBI polygraph examination in February, he tried to hide evidence by deleting more than 1,000 files containing millions of lines of codes, the New York Times reported today.

The FBI discovered the deleted files in March, after Lee gave the bureau permission to search his office computer. The administrator of the computer systems at Los Alamos then helped the bureau to re-create the deleted files. Officials say that after the polygraph test, Lee, apparently aware that investigators were suspicious of his computer use, deleted between 1,000 and 2,000 files.

The Times reported that experts from the FBI and Los Alamos said they were horrified when they began to sift through the files that they say Lee transferred and then deleted. He had downloaded what amount to the keys to the American nuclear arsenal, officials said.

The computer codes and data were, in effect, the distillation of more than a half-century of research on how to perfect nuclear weapons, they said.

The security violations are unprecedented, potentially exposing some of the nation's most dangerous secrets. Energy Department officials caution, however, that they still have no evidence that anyone accessed the data through Lee's unclassified office computer.

"This kind of egregious security breach is absolutely unacceptable," Energy Secretary Bill Richardson said in a statement.

Of particular concern is why the Justice Department denied a request by the FBI in 1997 to surreptitiously access Lee's computer. The FBI did not discover the classified data on Lee's computer until March 30 this year, after its suspicions of Lee had been made public and it was finally granted access. That discovery came nearly three years after the FBI began reviewing suspicions that Lee was passing nuclear secrets to the Chinese.

Employees at Los Alamos say that computers at the laboratory are considered government property and therefore can be inspected at any time by the Energy Department, which owns the computers.

"Everyone who works at the laboratory knows that their computers and their offices are the property of the government, period," a Los Alamos official said.

Yet FBI officers needed a court order to access Lee's computer. Energy Department managers have the right to access their employees' computers on their own accord. Had they been running the investigation, they might well have done so. But after consulting with the FBI, they decided they were no longer in control of the investigation and thus had lost their right to examine the computer without a court order.

And Justice Department officials said the FBI did not have enough credible evidence to merit such a search warrant.

In the convoluted saga of the Lee investigation, this legal loophole may have been just one that Lee slipped through during his years of security infractions. President Clinton's own initiative to thwart the spread of nuclear weapons may have inadvertently led to one of the greatest nuclear proliferation threats in decades, an administration official and arms-control analysts say.

At the height of Lee's alleged activity, the Taiwanese-born scientist had been working on the Clinton administration's stockpile stewardship program. This program was designed to move the nation's nuclear weapons scientists away from explosive underground testing and toward computer-based research. That work apparently gave Lee access to computer codes spanning virtually the entire history of the U.S. nuclear weapons program.

"There were substantial amounts of material transferred, just a huge compromise of nuclear security," acknowledged an administration official. "There's no question what he was doing was part of the stockpile stewardship program."

Few nuclear weapons experts doubt the potential damage of Lee's actions. The computer programs -- or legacy codes -- calculate, step by step, how a nuclear weapon explodes. And they can be used to test the feasibility of new nuclear weapons designs, as well as to improve existing nuclear weapons.

The connection between the potential breach and the president's nuclear nonproliferation policies is particularly sensitive.

"The legacy codes embody a very significant core knowledge base, developed over generations of nuclear experts," said Matthew G. McKinzie, a former Los Alamos researcher now at the Natural Resources Defense Council. "For that to get transferred outside the country would be a proliferation debacle of enormous proportions."

Energy Department officials flatly deny any connection to the administration's stockpile stewardship program and Lee's activities. They say nuclear weapons scientists were moving toward simulating nuclear explosions on computers long before Clinton came into office pushing a nuclear test ban. They say Lee began transferring data from Los Alamos' secured computer network to its unclassified network in 1983, when the Reagan administration opposed a test ban. He apparently ended his activities in 1995.

But the height of his alleged activities came in 1994 and 1995, just as the Clinton administration was drafting the test ban and launching what has become known as the archiving project.

But nuclear weapons scientists and some members of Congress said the United States could not maintain its own nuclear arsenal without testing. So the Clinton administration developed the stockpile stewardship program. It would harness the power of new research facilities, giant lasers and the most powerful supercomputers in the world to help scientists better understand how nuclear weapons work and how aging will affect their viability over time. The program cost is nearing $4.5 billion a year.

Part of that program involved updating old nuclear weapons designs -- developed on antiquated computers with outdated computer languages -- to run on modern supercomputers. The program has become more vital, as the nation's cadre of nuclear weapons designers ages and retires, leaving behind antiquated nuclear weapons computer programs that could be incomprehensible to a new generation of designers.

It was on that archiving project that Lee was working at the height of his alleged efforts to move data to his unsecured computer, an Energy Department official said yesterday.

"There are many intersecting things" between Lee's work on the computer initiative and the security breach, said Robert S. Norris, a nuclear weapons expert at the Natural Resources Defense Council. "There has been an enormous effort to accumulate all this data. That's why he had access to all this data."