The White House plans to replace Dr. W. Eugene Mayberry, chairman of the presidential commission on AIDS, with retired admiral James D. Watkins, a member of the commission, sources said yesterday.

Mayberry, 59, the endocrinologist who is chief executive officer of the Mayo Clinic, has expressed unhappiness over the amount of time the chairmanship of the 13-member panel requires. He has said White House officials told him in June when he accepted the job that he would need to come to Washington only a few days every month.

Sources said Mayberry plans to talk to White House chief of staff Howard H. Baker Jr. today. Mayberry said last week that he offered to resign in September after dismissing Linda Sheaffer, the executive director he hired in August.

A White House spokesman yesterday denied that Mayberry has resigned. Commission staff, who fielded a score of telephone calls from reporters and commission members, said Mayberry has told them he has not resigned.

Mayberry did not return repeated telephone calls to his Rochester, Minn., office yesterday. Several commission members said they had heard rumors of his departure but that Mayberry had not talked to them. Watkins, former chief of naval operations, could not be reached for comment.

The 13-member commission, which is charged with advising President Reagan on controlling the spread of acquired immune deficiency syndrome, has been criticized for the amount of time it has taken to get organized. Mayberry's leadership has come under fire from commissioners who say he is a poor administrator who has been unable to set priorities or hire a staff.

The first report of the commission, charged with advising Reagan about the disease's "medical, legal, ethical, social and economic impact," is due Dec. 7. Its final report is due in July.

The commission has been without an executive director since Sept. 11, after its first meeting in Washington, when Mayberry reluctantly fired Sheaffer, whom he had hired three weeks earlier. Panel members had complained to him that Sheaffer lacked expertise in AIDS and administrative experience. Others said they had learned about the agenda for a forthcoming meeting in the press.

Sheaffer, 38, said Mayberry asked her to resign "because of internal disagreement in the commission that had nothing to do with my overall performance."

In an interview last week, Mayberry said that when he fired Sheaffer, he told White House officials he too would resign but that his offer was not accepted. "I said if it wasn't working out, I would be pleased to leave," he said.

Several commission members have said they are alarmed about the lack of an executive director and the fact that only three of 15 permanent staff members have been hired.

They said the commission cannot afford to be perceived as floundering. Some said they are especially concerned about their reputations because the credibility of the panel has been criticized by public health officials and gay-rights activists for its lack of expertise about AIDS and the views of several members.

Others said their fears were not allayed after a meeting last week on Capitol Hill about pending AIDS legislation. Nearly a dozen legislators appeared to discuss a variety of bills with which the panelists were unfamiliar because of inadequate staff preparation.

While some sources suggested that Mayberry is a victim of infighting on the commission, others said that his management style and lack of Washington experience are more critical factors.

"I like the guy and he's sincere, but he has had that job for four months and we are still exactly nowhere," said Frank Lilly, a New York geneticist.

Dr. William B. Walsh, founder of Project Hope, an international health-care organization, said Mayberry "made what must have been a very difficult decision."

"In selecting Admiral Watkins I believe we have an oustanding leader of proven capability who will galvanize the commission," said Walsh, who has served on four previous presidential commissions.