New York's Cardinal John J. O'Connor yesterday said he might resign from the presidential AIDS commission if he felt his other responsibilities, including his work with AIDS patients, left him too little time or if the advisory panel was "simply heading in the wrong direction."

O'Connor's announcement came at the conclusion of a two-day meeting in Washington, the first under the leadership of its new chairman, retired admiral James D. Watkins. A former chief of naval operations, Watkins was elevated to the chairmanship by the White House last week after Drs. W. Eugene Mayberry and Woodrow A. Myers Jr. resigned as chairman and vice chairman, respectively, citing infighting and ideological differences among the panelists.

O'Connor said that although he found the panel's problems disconcerting, he is worried that he might be unable to devote sufficient time to the commission. O'Connor did not clarify what he meant by the "wrong direction."

"I must be realistic about my other responsibilities," said O'Connor, who regularly visits AIDS patients at hospitals operated by his archdiocese. "This spot should be considered available to the chairman to have someone who will really contribute the most." O'Connor also said that "maybe I could do more back in New York than on a national commission."

O'Connor, who praised Watkins, a longtime friend, also defended Mayberry, who has been criticized by other members as a weak administrator. "I think it would be very unfair to blame the problems on Dr. Mayberry," O'Connor said.

O'Connor's departure would be a serious blow to the commission, which is charged with advising President Reagan on the ethical, legal, social, medical and financial impact of the disease. The White House has not filled the vacancies left by the departure of Mayberry and Myers, and panel member Frank Lilly, a geneticist and the only openly gay member, said he might resign if he finds their replacements "deeply insulting."

The commission has been criticized for its lack of expertise about acquired immune deficiency syndrome and the controversial views of several members. Earlier this week, a coalition of groups led by the American Civil Liberties Union filed suit against the panel, claiming that it violates federal law because it lacks ideological balance and members of groups most affected by its work.

Watkins mentioned the commission's problems several times. "We are still in the stumbling process . . . nine weeks behind," he said, adding that he "has been given the freedom to do anything I think we need to make this commission work" by the White House.

He appointed several working groups on international AIDS and health-care financing and said he plans to move quickly to establish an advisory committee composed of AIDS doctors.

Watkins revised the schedule, indicating that the panel will probably meet at least once a month, not bimonthly as Mayberry indicated. Watkins also changed the location of next month's meeting from New York to Miami, a trip being arranged by Dr. Burton James Lee III, a Manhattan oncologist.

Lee told panelists he thinks a visit to Miami, which has reported more than 1,200 AIDS cases, will be useful because of its Haitian community, "unusual racial mix" and problems with "violent crime," and drug trafficking, which, he said, "as anybody who follows 'Miami Vice' knows . . . is totally out of control."

Panel members said that they were pleased by Watkins' leadership and hoped O'Connor will remain on the commission.

"It's an awful lot of progress compared to what we had before," Lilly said.