In a move that is already generating controversy, the Reagan administration is trying to repeal the National Cancer Institute's special authority to submit its budget directly to the president rather than through normal bureaucratic channels.

The change is contained in a large funding bill for biomedical research introduced this week by the Senate Labor and Human Resources Committee chairman, Orrin G. Hatch (R-Utah).

The proposal was made despite last-minute private protests by outside supporters of the federal cancer research program, who fear that it will "downgrade" the special status the cancer institute received when the national "war on cancer" was declared a decade ago.

While the administration describes the change as one of "increased management efficiency," Dr. Robert V. P. Hutter, president of the American Cancer Society, considers it a "symbol" that causes him "real concern."

"It's a retrogressive step, an expression of a lack of interest and the beginning of dismemberment of the national cancer program," he warned in an interview.

An aide to Hatch expressed surprise at the flurry of outside complaints that have already come from the ACS and cancer research centers, saying the proposed change was simply an effort to treat NCI the same as the other divisions of the National Institutes of Health.

"If the researchers feel threatened by this, I see little justification for it," said the Senate staff member, insisting that it was not meant to be a criticism of the cancer program.

The proposed bill, drafted in consultation with the Health and Human Services Department, would delete a provision in the 1971 "war on cancer" act that allowed NCI to submit its budget directly to the president. Other special powers include presidential appointment of the director and a cancer advisory board, as well as a three-member President's Cancer Panel.

This was a compromise worked out at the time between those who wanted a totally independent National Cancer Institute and those who argued that it should not be separated from the National Institutes of Health.

At a congressional hearing Wednesday, Edward N. Brandt Jr., assistant secretary of HHS for health, endorsed the deletion of the "budget bypass" provision.

Administration sources indicated, however, that top NCI officials were apparently unaware of the administration's position until Tuesday afternoon. The attempt to repeal the special NCI budget provision was apparently made at the direction of the White House Office of Management and Budget, said one source.

Another called the negative reaction by the cancer research community "overblown."

In practice, the change probably would make little difference. In recent years, two budgets have been drafted within the administration. While the NCI submitted a special budget request to the White House, another was prepared through the normal departmental process at HHS and was usually the one endorsed by the administration.

At present, NCI--with a budget of over $940 million--gets the largest single share of the 11 major disease divisions at NIH. A Hatch aide said this year's proposed authorization would give NCI a "handsome" 6 percent boost in funds, twice what the administration asked.