An employee at a Pennsylvania nuclear fuel plant was startled last year when one of the plant's janitors confided during a barroom conversation that fellow workers were smuggling highly enriched uranium out by concealing it in their crotches.

A hasty investigation turned up nothing to confirm the janitor's report. But an alarmed Nuclear Energy Commission, which oversees the nation's 76 licensed nuclear plants, ordered every worker leaving a nuclear security area anywhere in the country searched by either a scanning machine or a physical "pat down."

The pat-down searches were quietly dropped last month. Not because there was any less opportunity to steal nuclear material, officials said, but because workers at nuclear plants in Maryland and Wisconsin had complained that the searches were not only offensive but also a violation of their civil rights.

The issue of body searches is only part of a thicket of complex questions that has grown up for officials trying to determine how to protect the burgeoning and highly vulnerable nuclear industry and still not tread on civil liberties.

By 1985, according to some industry estimates, the United States will have as many as 168 nuclear-fueled plants with a corresponding increase in the potential for sabotage, theft or terrorism.

"If someone runs off with a substantial amount of this stuff from one of these plants," said a top NRC official this week, "you are probably going to go out and break down all the doors in America to get it back.

That possibility is beginning to trouble a growing number of civil libertarians, security experts and others connected with the nuclear field.

So far federal experts admit they have concentrated on developing elaborate plans to cover any contingency that might arise from a nuclear terrorist attack. NRC regulates the thickness of plant walls, the number of guards and the types of weapons that should be kept ready in case of an attack. But the rules say little about the rights of those who might get in the way during a terrorist incident.

Take, for example, this scenario: a report comes in of a theft of weapons-grade uranium from a nuclear plant. A short while later a message arrives from an unknown group claiming responsibility and threatening to detonate a crude nuclear bomb in a crowded area if demands aren't met.

The FBI, local police and quite possibly the military would be mobilized. Suspects might be rounded up on the street and forcibly interrogated. Phones might be tapped. If only a general idea existed of where the stolen material was a door-to-door search might be started - without search warrants. Cars leaving the area might also be s stopped and searched. Federal experts acknowledge that all these steps and more might conceivably be taken in a frantic effort to prevent catastrophe with civil liberaties being brushed aside.

"I have a strong fear that in the event of an actual incident ignored," said John H. Barton, a Stanford University law professor who has studied the problem for the NRC.

In a report for the federal agency two years ago Barton warned the only way to avoid the possibility or extra-legal measures arising in an emergency is to draw up the ground rules in advance.

But he added, during an interview this week, such guidelines pose problems for civil libertarians. "By facing the issue before it happens I'm afraid you could end uo weakening constitutional rights," Barton said. "But if you don't face them then the police could do something in an emergency that could be upheld later by the courts as an act of necessity."

That stretching of the law, Barton said, could have serious civil rights consequences in later years.

Some of the more vehement nuclear opponents like Ralph Rader and his supporters are already claiming that as the energy economy shifts to nuclear unprecedented intrusions on civil rights are already under way.

"The nuclear industry and the NRC have been like ostriches hiding their heads in the sand over problem," said Richard Pollock, head of the antinuclear Critical Mass project in Washington.

Last February when the NRC announced a tough new set of security rules for its licensees the federal agency admitted there was no evidence that any organization exists in the United States today with "the motivation, skill and resources" to attack a nuclear plant.

The assurance has not led federal security officials to let down their guard. The NRC gets a steady flow of information on potential nuclear threats from the FBI and other federal intelligence agencies and is studying an information "filter unit" to alert utilities and local police if there is a danger.

"Even a simple clearinghouse on a nationawide basis can cast a pall over people's lives," says one senior NRC offical. "But the alternative is to let the companies do it themselves and that less procedure safeguards. These are hard decisions"."

Intelligence gathering by private nuclear licensees goes on all the time and some experts fear it may be the greatest danger to civil liberties. Federal officials claim there is little they can do to check private snooping and with no official privacy laws in operation companies can circulate information - accurate or inaccurate - at will.

In July, for instance, security experts from utilities across the country gathered in Boston for a day-long seminar on an unorthodox, sit-in held last May in Seabrook, N.H., be a group called the Clamshell Alliance. The peaceful demonstrators tied up New Hampshire courts and worked at the Seabrook nuclear site when 1,414 let themselves be arrested and carried off to jail.

Organizers of the Boston conference said it was held to discuss tactics, not exchange names or security intelligence on members of the Clamshell group, which has formed chapters around the country.

Still, at least one out-of-state security official who took part said he came away with new intelligence information on the group for his files. And the New Hampshire state police, who ran the seminar, list in their intellgence files inaccurate information on the Clampshell organization, including one note that informants said the sit-in was only a cover for "terrorist activity" and that the group might include bombers.

A source for the New Hampshire police files on the Clampshell Alliance was John H.Rees, a publisher of a small Washington-based newsletter that provides information on dissident groups - including nuclear opponents - to police departments and at least one utility - the Georgia Power Co.

The Atlanta utility used information from Rees and other sources to build sophiscated intelligence files on the individuals and groups ranging from anti-nuclear activists to opponents of utility rate hikes, according to former members of the company's security staff, Georgia Power says it mantains its security operation to meet NBC requirements.

Nuclear industry trade groups have also apparently gathered files on their opponents. A spokesman for the Atomic Industrial Forum said his group maintains a "mini-morgue" with information on nuclear opponents for its members. The morgue contains "clippings and notations," he said.

According to a Potomac Electri Power Co., memo in 1973, the AIF and another utility trade group, the Edison Electric Institute, called on utility companies in eight U.S. cities to attend and report back on meetings of Another Mother for Peace, and antiwar organization that had decided to oppose nuclear power.

"We go to the opposition's meetings spokesman.

How far such information gathering in the name of nuclear security should or does go is not clear.

"It is a legitimate quest becaues of the climate of the time," said a New England utility security man.

"In 90 per cent of the cases it's none of their business," said Rep.John Moss (D-Calif.), whose House Commerce subcommittee on oversight and investigation is considering an investigation of the nuclear intelligence field.

And a top security official for the NRC admits that there may be invasions of civil liberties and privacy in the name of security. "It's a question of what do you want," he said. "A safe reator or happy people."