An extensive review of security at the nation's nuclear weapons plants, covering everything from guards at the gates to transportation of warheads, exposed deficiencies in training, discipline and planning that require "a program for positive improvement," the Energy Department announced yesterday.

There was no indication that the study uncovered any security breaches that threaten public safety or jeopardize national security, but the findings prompted Energy Secretary James D. Watkins to issue a 15-point order reorganizing the department's security procedures.

"We found nothing to indicate a breach that would harm U.S. interests, no bleeding wounds," said retired Army Maj. Gen. James E. Freeze, who headed the investigative team. But he said his classified report to Watkins "provides over 300 recommendations" for security improvements.

Watkins directed Undersecretary John C. Tuck to make "prompt organizational and procedural changes," including the removal of overall security responsibility from the department's Defense Programs office, which runs the nuclear weapons complex.

Tuck said at a news conference that Watkins was warned by members of Congress during his confirmation hearings early in 1989 that he would find longstanding security problems at the 17-factory, 12-state complex that produces the nations's nuclear weapons.

A security study already under way at that time "just wasn't answering the mail," Tuck said. So Watkins directed Tuck to undertake a new one, and Tuck hired Freeze, a career intelligence officer who was formerly second in command at the National Security Agency, to conduct it.

The Energy Department spends more than $1 billion a year on security at the weapons complex.

The so-called "bomb factories" have a long history of embarrassing security breakdowns, ranging from inability to account for small quantities of plutonium to unauthorized admission of visitors from a Warsaw Pact country to a secure area.

In the time Freeze and his team were visiting the sites, the department acknowledged that it was unable to account for a small amount of the essential radioactive gas tritium at its Oak Ridge, Tenn., plant, and that an inspection of the Rocky Flats, Colo., plant detected unauthorized transportation of plutonium by workers who were allowed to remove their metal toed-boots to pass through metal detectors.

The "executive summary" of Freeze's investigation that he and Tuck released yesterday gave no details of any of the security problems and omitted mention of any specific site.

But Freeze said that conditions at Rocky Flats "caused us to have an apoplectic seizure." The Energy Department recently stripped the civilian company that operates Rocky Flats of responsibility for security and gave it to a firm that specializes in security, Tuck said.

Freeze said he was "by and large favorably impressed with the protection forces," or guards, at the plants. He said the team found "tremendous improvement" in gate security and the "intrusion protection system."

But his report said an attempt to conduct an inventory of the complex's classified documents "has resulted in an unsatisfactory condition."

Tuck acknowledged that "we won't be able to account for every secret document."

Tuck and Freeze reserved their strongest language for the security clearance system for employees. Tuck called it "absurd" because clearances, which are costly and time-consuming to process, cannot be transferred with an individual from one site to another but must be repeated.

Freeze said he was "absolutely aghast at what we found in personnel clearances." He said it takes up to 410 days to process a Q clearance, the highest category. During that time, he said, qualified employees who are on the payroll but cannot work until they receive clearances tire of living "outside the fence in the leper colony, so they leave."