Dr. Christopher Fordham III, a North Carolina medical, dean slated to become the government's top doctor, has rejected the job after spending a month working in it and finding he would have little authority.

Sources at the Department of Health, Education and Welfare said yesterday that Fordham - who was HEW Secretary Joseph A. Califano Jr.'s choice as assistant secretary of health - suddenlu left his desk after a session with Califano Wednesday, cancalled appointments at the White House and Congress, and flew home.

Late yesterday afternoon Califano released an exchange of letters in which Fordham said he was leaving "for deep personal reasons." Califano replied, "I believe you would have made an excellent member of the health team". I am please that you will continue to serve (on) my advisory committee on national health insurance issues."

Despite the polite language, one-well-informed souce said, "Fordham quit after severe disagreement with the secretary."

Fordham did not return a reporter's phone calls, and Mr. Fordham - reached at the Cahpel Hill home of the University of North Carolina Medical School dean - would say only, "I'm in the predicament of not being in a position to dicuss it."

Fordham was still only assistant secretary-designate, awaiting clearances. But he had been an HEW consultant for a month, in effect filing the job,.

He was doing so after three prominent doctors turned it down - in part because they felt it had been rendered "toothless," they told friends.

The Fordham incident is the latest in a series that has stirred dissension among health officials and medical scientists.

"The direction of health affairs in the government is in chaos, but don't quoted me or I'll be out," the head of one major health agency in HEW said. "Medical care is in disarray in this country, in part because there was no health leadership during the Nixon and Ford years.

"But so far it's another mess now. No one's in charge of health policy except Mr. Califano, and he can't do it all."

Califano took office as the "H" forces in HEW had been severely shaken by the Ford administration's swine flu experience - recommending mass shots for a disease that never appeared, then being forced to call them off because some caused paralysis.

Califano rapidly fired then-assistant Secretary for Health Dr. Theodore Cooper and several other agency heads, including Dr. David Seccer head of the Center for Disease Control that ran the swine flu program.

He kept Dr. Donald Fredrickson, head of the National Institutes of Health, and promised to "depoliticize" NIH. But in the poast few weeks many NIH scientists have been angered by Califano, that demands a sharp cut in the number of scientific advisers who help NIH allocate medical research funds.

Also, Medicare and Medicaid and attempts to monitor medical quality were put under a new Health Care Financing Administration reporting directly to Califano.

"All this was done without involving an assistant secretary for health. I think Fordham woundered what there was for him to do in the future," a high HEW official said.

A health agency head said, " Califano assured Fordham he wasn-t being downgraded, but meanwhile he was planning to reorganize Fordham's agencies and using other people to screen health job candidates."

Before Fordham agreed to take the assistant secretary's job in mid-march, it was turned down by Dr. David Hamburg, head of the Institute of Medicine at the National Academy of Sciences; Dr. Charles Sandler, director of famed Massachusetts General Hospital, and Dr. William Roy, Former Democratic representative from Kansas.

Many members of Congress and groups, including the American Medical Association, have said health, education and welfare are too much for anyone to direct, and have urge welfare are too much for anyone to direct, and have urgeed creation of a Cabinet-level agency for health alone.