The presidential advisory commission on AIDS, meeting for the first time yesterday before an often contentious audience of AIDS patients, gay-rights activists and federal officials, got a sense of how difficult its task will be.

The 13-member panel, charged with advising President Reagan on how to control the spread of acquired immune deficiency syndrome, heard from more than a dozen witnesses who discussed the difficulty of reaching intravenous drug abusers and minority groups most at risk, deplored the slow pace of federal research and education efforts and questioned the credibility and competence of the commission.

The tone for the meeting was set by the first speaker, Secretary of Health and Human Services Otis R. Bowen who bluntly stated that he was "extremely disturbed" by harsh words from "some self-appointed critics" of federal efforts to combat AIDS. "To criticize this effort is counterproductive and mean-spirited and tends to tarnish what is a solid record of accomplishment in modern medical science and health policy," Bowen said. He did not name those critics, but his spokesman later said he "assumed he was referring to anyone who's trashing the federal government."

Gay-rights activists and some scientists have deplored the pace of federal educational efforts and the time it takes to approve drugs. Conservatives and several members of the AIDS commission have criticized federal officials for inadequate efforts to protect the blood supply or failing to endorse widespread mandatory testing or that infected children be barred from public school.

Bowen, who praised top federal AIDS officials by name, traced the progress of the federal war on AIDS from the first cases identified in 1981 to the vaccine trials under way at the National Institutes of Health.

"I welcome you to the fray," he said, smiling slightly at the panelists who looked uncomfortable under the relentless glare of klieg lights. "I promise you every assistance. And I wish you the very best in your work. We need all the help we can get."

For much of the day a group of about 75 protesters from a New York-based group called ACT UP (AIDS Coalition To Unleash Power) staged a peaceful protest outside the National Press Club where the meeting was held. Security officers inside the auditorium were braced for an expected disruption of the meeting. There were no arrests. There were occasional boos and hisses, as well as sniggering that sometimes punctuated statements by commission members.

Dr. W. Eugene Mayberry, chairman of the panel, repeatedly pleaded with the audience not to judge the panel too quickly. "We believe we have the capacity to help or we wouldn't be here," he said.

Mayberry said he was not certain which issues the commission will focus on in its attempt to meet its charge to advise the administration on the "medical, legal, ethical, social and economic impact" of the disease that has struck more than 42,000 Americans. Mayberry said the commission, which is scheduled to meet bimonthly, was trying to build on existing information "not reinvent the wheel."

Stephen Beck, a founder of the National Association of People With AIDS, urged the panel to seek out those infected with AIDS "because there are none on this commission." He said he hopes the commission will "take the lead in mitigating the hysteria gripping this country."

Frank Lilly, a geneticist and the only openly gay member of the panel, drew applause when he asked a group of speakers who were supposed to represent interest groups why there was no organization representing homosexuals was on the program.

One of the most impassioned speakers was Michael Petrelis, a New York man who has had AIDS for more than two years. "I may not be around to see your final recommendations," he said. ". . . How can I have trust in this commission when its homophobia and medical ignorance is well documented?"

Petrelis was referring to several panelists whose views on AIDS are controversial and diverge from accepted scientific evidence.