WASHINGTON (AP) _ Lax protection of high-grade plutonium and other nuclear arms material is emerging as one of the most serious, though least well-known, flaws in the Energy Department's troubled weapons program.

Compared to highly publicized mechanical breakdowns, management failures and environmental violations at the nuclear weapons plants, little has been documented of security lapses and efforts to correct them.

Most official information about protection of nuclear materials, including plutonium and enriched uranium, and of stored weapons containing the materials, is classified. Only people holding special security clearances are allowed inside areas of weapons manufacturing plants and laboratories that hold the materials. Several key weapons plants are shut down temporarily for safety reasons.

Evidence is now growing, however, that despite the weapons makers' devotion to secrecy, some federal nuclear facilities have run the risk in recent years of allowing the theft of enough plutonium to build a nuclear bomb.

Members of Congress are suggesting that some Energy Department officials have soft-pedaled the protection problems. Some department officials complain that budget constraints have prevented the filling of security posts with adequately trained people.

Among security flaws disclosed this week by a House Energy investigations subcommittee:

-Argonne National Laboratory-West, near Idaho Falls, Idaho, violated rules last year on controlling access to portable plutonium at a nuclear reactor site at the lab.

Details of the incident are classified, but a senior Energy Department official told a closed hearing of the subcommittee that the violation ''revealed a deficiency and vulnerability'' to diversion of bomb materials to terrorists.

Portions of the hearing transcript were declassified earlier this week.

The official, Hilary J. Rauch, manager of the regional Energy Department office that manages the Idaho facility, did not dispute a suggestion by Rep. Gerry Sikorski, D-Minn., that the incident meant ''people could be carting plutonium out of the place.'' Rauch stressed that the problem has since been corrected.

-Quantities of plutonium large enough to make a nuclear bomb were left unattended in rooms without alarms at Lawrence Livermore National Laboratory last spring.

A previously secret inspection report on Lawrence Livermore also said large quantities of plutonium ''were often left, between process steps, with only one person or unattended'' during normal business hours. Department officials acknowledged to the House subcommittee that this was a serious lapse of security.

-A senior department official, Brig. Gen. Paul F. Kavanaugh, expressed concern in an internal memorandum last April at the frequency of ''marginal and unsatisfactory ratings'' of nuclear materials security by federal inspectors of weapons plants.

''If, within the DOE, we cannot articulate and enforce effective security practices at our most sensitive facilities, we will deserve the comments of our most vocal critics,'' wrote Kavanaugh, who left the department shortly after sending his memo.

Kavanaugh also drafted a tough-worded message that he suggested be sent to managers of key weapons plants requiring immediate action to improve nuclear materials security. A few weeks later a brief version of his proposed message was sent offering thanks for previous efforts but making scant mention of the problems.

The subcommittee is now investigating why the Kavanaugh draft message, which the panel called the first honest acknowledgement by the department of the breadth of its security failures, was watered down by his superiors.

Rep. John Dingell, D-Mich., chairman of the investigations subcommittee, has charged that the department failed to ensure adequate security at the Los Alamos National Laboratory, one of the most sensitive sites in the nuclear weapons complex, during a labor strike last spring by the lab's private security force.

The department denied that security was compromised, but it acknowledged that substitute security personnel did not meet department qualifications.

Security questions also have arisen at the Oak Ridge weapons complex in Tennessee. Dingell expressed alarm that responsibility for granting security clearances was taken away from Oak Ridge's security officials and given to the personnel office.

Also, a laboratory at Oak Ridge was unsure for more than a year, starting in August 1988, whether a substantial amount of tritium - a gas used to make nuclear warheads - had been stolen from a loading facility. The department said last week that it was now confident none was lost, but some members of Congress say doubts remain about Oak Ridge's ability to protect tritium supplies.