WASHINGTON (AP) _ The executive director of President Reagan's advisory commission on AIDS, Linda D. Sheaffer, resigned abruptly after the panel's chairman asked her to leave, government officials said.

A White House official said Monday that concerns about Sheaffer stemmed from friction between panel members and the commission's chairman, Dr. W. Eugene Mayberry, who had chosen Sheaffer for the job.

''Some of the commissioners have been a little put out as to what they perceive as Mayberry's heavy-handed running of things, so this may be a symbolic deal,'' said the official, who demanded anonymity. ''There was grumbling about his hiring her without any input (from other commissioners).''

The official said some panel members also had criticized Sheaffer's work.

''I did hear a lot of complaints by committee members that they didn't like her work; they weren't getting enough chance for input on witnesses or where they would hold hearings,'' he said.

Sheaffer, a government health officer who had headed the federal Office of Organ Transplantation before she was loaned to the AIDS Commission, left the panel job Friday, said another government official who also demanded anonymity.

Attempts to reach Sheaffer on Monday night were unsuccessful, but The New York Times and The Washington Post, which reported on the resignation in today's editions, said she confirmed that she was leaving in interviews Monday.

''After the recent meeting of the commission, the chairman asked that I resign,'' she said, reading a prepared statement. ''He did so because of internal disagreements within the commission that had nothing to do with my overall performance as the executive director.''

She declined to give details on the disagreements, saying, ''To discuss it further will only do further damage to the commission. It proves to me how frightened everyone is that they won't be able to complete the job assigned to them.''

Mayberry, who is chief executive officer of the Mayo Clinic in Rochester, Minn., did not return a call to his home Monday night.

The Times reported that Mayberry had argued initially against demands by fellow panel members that Sheaffer be replaced, but he yielded to pressure eventually and asked her to resign.

He told the Post that he has ''a great deal of admiration and respect'' for Sheaffer, but that ''under the circumstances, it seemed best'' that she leave.

The AIDS Commission, appointed July 23, has a year in which to compile a final report on the nation's programs to combat acquired immune deficiency syndrome.

As of Sept. 7, AIDS had been diagnosed in 41,735 Americans and more than half of them, 24,019, had died, the Centers for Disease Control reported. No one is known to have recovered from AIDS.

The newspapers reported that several commissioners said the desire to replace Sheaffer stemmed from a need for a more effective staff.

''I'm worried that we're a couple of months into this and we're still lacking structure and organizational spine,'' panel member Dr. Burton James Lee III, a physician at the Memorial Sloan-Kettering Cancer Center in New York City, told the Post. ''Somehow this thing has got to get off the ground.''

''For whatever reason, lack of staff or whatever, things just weren't happening,'' Lee told the Times. ''With Gene Mayberry out in Rochester, Minn., most of the time, the commission felt we had to get a really good, high- powered full-time person'' to lead the staff.