Health, Education and Welfare Secretary Joseph A. Califano Jr. broke a 12-year-old pattern yesterday by appointing a nonphysician as commissioner of the Food and Drug Administration.

The new commissioner is Dr. Donald Kennedy, a professor of human biology at Stanford University. His appointment does not go to the Senate for confirmation.

Kennedy, 45, is the first nonphysician since 1965 to hold the top FDA job. The last four commissioners have been medical physicians.Kennedy holds a doctorate degree.

FDA critics have contended that physician-commisioners have tended to be biased in favor of drug manufacturers and makers of medical devices, whose industries are regulated by the FDA.

"Doctors generally are taught that drugs are good, and that's the point of view many of them keep," said Dr. Sidney Wolfe, a FDA critic who heads Ralph Nader's Health Research Group.

Kennedy, however, is the fifth non-physician to serve as FDA commissioner. Four others served in that post between 1940 and 1960.

A spokesman said yesterday that Califano "looked at everybody" in his search for an FDA commissioner. "He wasn't looking for a doctor or a nondoctor. He was just looking for the best qualified person," the spokesman said.

In his formal announcement, Califano praised Kennedy as "one of the nation's most distinguished scientists."

"He has the dedication to join with me in leading our nation's effort to ensure the safety and efficacy of the foods, drugs, cosmetics and medical devices used by our citizens," Califano said.

Kennedy has been a Stanford faculty member since 1960. His specialty is neurophysiology, which involves research on the physiology of the central nervous system.

Since Fall, Kennedy has spent time shuttling between Washington and his home in Palo Alto, Calif, in connection with his duties as a senior consultant to the White House Office of Science and Technology Policy.

Kennedy said he feels privileged to have been named to the new post. But he said he is entering the job without any major plans or illusions.

"I'm not coming in with an agenda," he said. "I'm not a man on horseback. I have a lot to learn."

Kennedy succeeds Dr. Alexander M. Schmidt, who resigned as FDA commissioner last November to return to the University of Illinois to be vise chancellor for health services. Schmidt had held the post since 1973.