In the face of opposition from scientists and universities all over the country, the House voted overwhelmingly yesteday to put the National Institutes of Health under closer congessional control.

NIH is a gigantic set of research laboratories in Bethesda and the dispenser of dollars that finance most of the nation's medical studies.

Government officials for years have promised to leave NIH largerly undistrubed and "unpoliticized" as a center of unbiased medical investigation.

But yesterday, Rep. A. Waxman (D-Calif.), chairman of the House Commerce health subcommittee, convinced the House that the agency -- as recipient of $3.4 billion this year in federal funds -- needs closer congressional oversight and direction.

By 292 to 48, the House voted to:

Require each of NIH's nine institutes -- each dealing with different diseases -- to come before Congress each year for budget authorization hearings.

Reguire each institute to seek renewal of its authority to exist after three years and presumably every three years thereafter.

NIH has long had permanent operating authority, with the president asking for a sum for each institute every year and congressional appropriations committees making what has amounted to the final decision.

The only change came in 1971 and 1972 when Congress ordered "crusades" against cancer and heart disease. It established annual authorization hearings and periodic renewals of authority for NIH's two largest units, the National Cancer Institute and National Heart, Lung and Blood Institute.

That action did nothing to fight cancer and heart disease and created "significant . . . delay and disruption," four former assistant secretaries for health under Presidents Johnson, Nixon and Ford said this month.

The Waxman bill has also drawn the opposition of eight major groups representing universities, medical centers, medical professors and researches, as well as the four doctors who headed NIH from 1950 to 1975.

After opposition to an earlier version, the bill has been supported by Secretary of Health and Human Service Patricia Roberts Harris and NIH's current director, Dr. Donald Fredrickson. Some federal officials say Fredrickson has been silenced by Harris on the issue, after some severe clashes with her.

The Waxman bill will next go to a conference committee. A Senate bill sponsored by Sen. Edward M. Kennedy (D-Mass), head of a counterpart health subcommittee, would keep the present NIH system, establish a President's Council for the Health Sciences to advise HHS and NIH and return the cancer and heart institutes to something close to their status before 1971 and 1972.

Waxman said yesterday he has "no criticism" of NIH research but thinks "congressional oversight and committment to NIH" would be strengthened by his approach.

The House also followed Waxman's lead in authorizing $4.07 billion for NIH in fiscal 1981, but a House appropriation Wednesday of just $3.6 billion made the $4.07 billion figure meaningless.