The executive director of the presidential advisory commission on AIDS has been fired after panel members complained to the chairman, Dr. W. Eugene Mayberry, that a lack of leadership and direction undermined the commission's first meeting here last week.

Linda B. Sheaffer, hired several weeks ago as chief staff member of the commission, was asked by Mayberry last Friday to leave the post. Sheaffer, who will return to her job as acting director of the federal Office of Organ Transplantation, said yesterday that she was "not surprised" by Mayberry's action, which came one day after the 13-member commission concluded a two-day meeting in Washington.

In a prepared statement, Sheaffer said Mayberry "asked that I resign . . . because of internal disagreement in the commission that had nothing to do with my overall performance as executive director." She declined further comment, saying that "to do so would only do the commission more harm than good."

Mayberry, chief executive officer of the Mayo Clinic, said yesterday that he has "a great deal of admiration and respect" for Sheaffer but that "under the circumstances it seemed best" that she leave. He declined to elaborate. No successor has been named.

Several commission members reached yesterday said that they were surprised by the speed of Sheaffer's departure. They said the group had told Mayberry they were worried that only half the 10-member staff had been hired and by Sheaffer's lack of expertise about AIDS. Others said they were miffed because they learned about the agenda for a forthcoming meeting in the press.

Their concerns about staff leadership were compounded, they said, by ideological divisions among the panelists and a general uncertainty and confusion about its role.

Several panelists said they were particularly concerned because the credibility of the commission, established to advise President Reagan about controlling spread of acquired immune deficiency syndrome, has been attacked by public health officials and gay rights activists. None has a background in AIDS and some panelists have expressed views that are controversial or diverge from accepted scientific evidence and public health practices.

"This is a high-profile commission," said Dr. Burton James Lee III, an oncologist at Memorial Sloan-Kettering Hospital in New York City. "I've made a 100 percent commitment to serving on this commission. I'm worried that we're a couple of months into this and we're still lacking structure and organizational spine. Somehow this thing has got to get off the ground."

Several panelists have said that they are particularly concerned because they believe their professional reputations are at stake. Several were upset that candidates they suggested for the staff director's job were not selected.

Dr. William B. Walsh, founder of Project Hope, an international health-care organization, and a veteran of four previous presidential commissions, said that although he thought Sheaffer "did the best she could" he regarded a strong staff director as essential if the panel is to meet its deadline of next July for a final report.

The panel, appointed July 23 by Reagan, is charged with advising the White House on the "medical, legal, social, ethical and economic issues" that AIDS presents.