Members of the president's 13-member AIDS commission yesterday endorsed a report by the chairman that calls for sweeping new programs to fight the epidemic.

But they questioned retired admiral James D. Watkins' estimates that controlling AIDS could cost an additional $2 billion annually in federal and state funds.

"I don't want want us to go flying off throwing money" at a variety of social problems, said commission member Richard M. DeVos, chairman of the Michigan-based Amway Corp. DeVos applauded the 60-page interim report released last week that surprised the advisory panel's critics, who hailed its forceful tone and detailed recommendations on expanded treatment for drug abusers and home health care for AIDS patients.

After President Reagan appointed the panel last summer to advise him on the epidemic, critics decried the group's lack of expertise in acquired immune deficiency syndrome and predicted the panel would have no significant impact.

Dr. William B. Walsh, founder of Project Hope, a nonprofit health care corporation, said he believed that implementing Watkins' 178 recommendations -- including providing "treatment on demand" for intravenous drug users, the fastest growing group of AIDS patients -- could cost five times Watkins' estimate, or an additional $10 billion a year. The federal government this year appropriated $951 million to combat AIDS.

When John J. Creedon, chief executive officer of Metropolitan Life Insurance Co. of New York, asked Watkins the source of the projected costs, which do not appear in the report, the former chief of naval operations displayed a flash of annoyance.

"We're not saying this is the definitive cost analysis," said Watkins, who said the commission's staff would be preparing detailed cost estimates to send to the White House next week along with the report. "I've talked to {Office of Management and Budget Director} Jim Miller, and these kind of numbers don't shock him."

The commission's executive director, Polly Gault, said $1.5 billion of the projected $2 billion in additional costs represents the National Institute of Drug Abuse's estimate of the expenses of providing treatment over a 10-year period for one-third of the nation's 1.2 million intravenous drug users.

Panelist Theresa Crenshaw applauded the report but said she hoped it would include a statement deploring the "harassment" of researchers who hold views contrary to widely accepted scientific evidence. Crenshaw, who has said in the past that she believes AIDS could be transmitted by mosquitos or casual contact, did not specify whom she meant.

Geneticist and panel member Frank Lilly sounded a note of caution. "Any new idea must be researched," he said, "but in every area there are always cranks and there are ideas that are pushed very hard that are not taken seriously."