Under order from President Carter, the National Institutes of Health has begun major cuts in its 169 outside advisory groups, stirring protests from some NIH officials and scientists that the groups play a major role in the agency and that their elimination will cause significant damage.

The cuts are in response to an Office of Management and Budget order to every Cabinet officer to, in effect, start implementing the President's campaign pledge to cut "1,900 agencies" to 200.

A White House fact book has disclosed that 1,185 of an actual 2,103 "executive branch agencies" are really advisory groups.

As one step, NIH Director Dr. Donald Fredrickson sent Health, Education and Welfare Secretary Joseph A. Califano Jr. a proposal Friday to reduce the 43 advisory groups of the big National Cancer Institute to 26 through eliminations and mergers.

But NIH's 169 advisory bodies --more than half of HEW's estimated 300 -- do far more than just chat about agency policies. They spent thousands of hours last year screening 10,254 applications by doctors and scientists for research grants in every field from asthma to yaws.

They "approved" 7,177, of which 3,940 of the highest-ranked were funded, contributing to a total NIH research grant outlay of $1.2 billion.

Some NIH scientists said last week that cuts as severe as those planned could "hurt us" and "make us more narrow." "They could force us to spend more of our time being administrators and less being scientists, and we could lose touch with the real world," one scientist said.

Dr. Norman Kretchmer, director of NIH's National Institute of child Health and Human Development and a working scientist himself until he left Stanford University for NIH in 1973, said, "NIH couldn't operate without peer review by outside committees. Countries like Canada, France and Britain have copied our system."

But Dr. Sidney Wolfe, head of Ralph Nader's Health Research Group and a former NIH scientist, said: "I was consulted by one of Califano's people last week. I said cutting the number of committees was a good idea. There's too much cronyism, too much of an old boy philosophy that winds up funding the same people and same ideas and prevents innovation.

"More grant review should be done in-house by NIH people themselves, with a few outside consultants. Review shouldn't be solely in-house, but it should be someplace in between the present huge megastructure and nothing at all."

NIH occupies a university-like campus in Bethesda which is in fact a combination of a research center, with scientists at laboratory benches and bedsides, and a network of administrative offices that dole out the bulk of a $2.5 billion annual budget to researchers elsewhere. there are 11 NIH research institutes in all, among them the cancer institute, the National Heart, Lung and Blood Institute, and the National Eye Institute.

Nobody in the Carter administration proposed any target number or goal for advisory committee elimination, NIH and HEW officials insist.

But one NIH source -- who, like many others, insisted on remaining anonymous -- said, "there was blood on the floor here. Early on, people thought they could eliminate just a few committees. But the word from high up was 'nothing doing'."

Dr. Thomas Malone, assistant to Director Fredrickson, acknowledged that "we did have to review our first justifications -- our descriptions of why we felt committees were needed. There wasn't complete satisfaction with them at first."

Fredrickson would not say how many of NIH's 169 advisory groups he now believes could be dropped or merged.

Another HEW source said, "It can't be as many as the cancer institute's; because some institutes are a lot leaner. But it's not going to be trivial either."

"OMB has indicated a desire on the part of the President to shape things up," Dr. James F. Dickson III, acting assistant secretary for health, summed up.

Hale Champion, HEW under secretary, said, "The White House called for a zero based review with all possible recommendations for reductions. We're asking every agency in HEW to respond. Even if they think they can't eliminate any groups, we're asking them to rank them in importance, so there'll be some basis for judgment by the secretary or White House on which ones can go."

"Advisory groups are not inexpensive," said Dr. Richard Tjelma, the cancer institute's assistant director.

NIH spent $12.2 million last year on its advisory apparatus: 12 general advisory groups mandated by Congress and the 157 others. Advisers get $100 a day plus expenses, and most grant-review groups meet three time a year for two days at a time.

The cancer institute spent $185 million last year on its 621 advisers and expects to save $800,000 by cutting committee memberships by 208 over coming months.

"We view what we're doing as an experiment," Tjelma said. "I think it will probably work. If it doesn't, if the work load for the remaining groups gets too heavy or if the quality of the reviews goes down, we'll recommend a change.

"All in all, we don't consider the change bad -- simply an attempt to get the government's work done more effectively."

But another NIH official said: "Wait until more NIH scientists and scientists around the country hear about this. After all, NIH is the country's largest single support of medical research. This is going to mean a reduction in the ability of scientists in general in this country to influence NIH and the directions of medical science."