Deputy Assistant Secretary of Energy Donald M. Kerr Jr., once a strong critic of President Carter's proposed comprehensive nuclear test ban treaty, yesterday was named the new director of the Los Alamos Scientific Laboratory, the nation's first nuclear weapons facility.

Kerr, 40, was appointed by the regents of the Universtity of California, which operates the New Mexico complex under a contract with the Department of Energy.

Last year, when he was acting assistant secretary of energy, managing the Department's nuclear weapons program, Kerr warned Congress that Carter's proposed five-year test ban treaty was dangerous because reliability of the nuclear stockpile could be endangered by a treaty of that length.

Carter subsequently adopted the three-year approach favored by Kerr and his predeccessor as director of Los Alamos, Dr. Harold Agnew, as well as the director of the government's other nuclear weapons development facility, Dr. Robert Batzell of the Lawrence Livermore Laboratory in California.

Kerr's appointment is certain to add to an ongoing debate within the university over whether the contract to run Los Alamos should be continued. The university has operated the facility since it was established by Dr. J. Robert Oppenheimer in 1943 as the site for development and production of the first atomic bombs.

Under the contract, the secretary of energy, currently James R Schlesinger, must approve the university's choice for a laboratory director.

Kerr, with past experience at Los Alamos in the nuclear testing area and a tour of duty in Washington helping direct the government's nuclear weapons program, was Schlesinger's choice for the job.

Critics of the Kerr appointment attempted to head it off by enlisting support from President Carter's science adviser, Dr. Frank Press. Press and others, however, reportedly were unable to come up with an alternative selection acceptable to Schlesinger.

Some university professors and students want Los Alamos to drop its weapons program and to concentrate on the peaceful uses of atomic energy. Weapons currently make up about 45 percent of the laboratory's operations, with health, energy and other nuclear research constituting the rest.

The university's discomfort with the weapons aspect of Los Alamos was ilustrated in the news release it issued yesterday. It referred to Kerr's present post as deputy assistant DOE secretary for energy technology, which he has held for only a few months, and made no mention of his years in the department as a key nuclear weapons official.

It also noted his 10 years at Los Alamos, but not the posts involving weapons and their testing. Instead, it listed only his last year there "as an alternate energy division leader."

With Livermore, Los Alamos does basic design research, development and testing of all proposed nuclear weapons.