Relatively few people took notice last week when a bill to make the commissioner of the Food and Drug Administration subject to confirmation sailed through the Senate.

Portrayed by its sponsors as a "routine" way to elevate the FDA commissioner to a level shared by heads of virtually every other regulatory agency, the legislation also had another purpose.

"This amendment would give the FDA an independent commissioner, appointed by the president and subject to congressional approval," said Sen. Albert Gore Jr. (D-Tenn.), a key supporter of the legislation. "An independent commissioner will answer to Congress and the American people, not to several other agencies in the administration."

Since the Reagan administration took office in 1981, FDA scientists have had to fight hard to retain a measure of independence. On several occasions, according to FDA officials, the administration has attempted to impose political goals that conflict with scientific policy.

The administration made two major changes affecting FDA. It transferred to the secretary of health and human services authority to decide important regulatory issues, and it empowered the Office of Management and Budget to review all agency regulations.

"Over the past seven years, we have seen again and again decisions FDA made based on scientific expertise reversed for political reasons and reasons of regulatory philosophy," said Mitchell Zeller, assistant director for legal affairs at the Center for Science in the Public Interest.

"This bill will at least make it more difficult and embarrassing for the administration to get away with that," he said.

On several occasions, FDA researchers have sought to ban a product or take action only to be overruled by the HHS or the OMB.

For example, FDA scientists said they wanted to ban interstate sale of raw milk, and the agency long ago sought to put labels on aspirin bottles warning of Reyes syndrome, a rare but deadly disease that can afflict youngsters who use aspirin.

The HHS overruled the agency on banning raw milk sales and delayed for two years the decision to require Reyes warnings on aspirin labels.

Administration and FDA officials declined comment yesterday because the legislation has not been passed. The House has approved another version of the bill, and differences must be resolved in conference.

The legislation will still require that FDA Commissioner Frank E. Young answer to the secretary of health and human services. But an amendment offered by Gore would permit Dr. Young to appoint his own scientific advisory boards, rather than continue to rely on appointments from the HHS.

"This bill is a step in the direction of restoring the independence of the FDA," said William Schultze, a lawyer with Public Citizen Litigation Group. "And that will help assure that important decisions relating to the safety of food and drug products can be made by scientists at FDA rather than politicians at HHS and OMB."

Last year, the FDA introduced rules that make it much easier for victims of life-threatening disease to obtain experimental new drugs. The original plan would have permitted patients to gain access to such drugs even before the FDA determined that they were effective.

To forbid their use, the commissioner would have had to prove -- at a very early stage in testing -- that they would not work.

Scientists, including many at the FDA, denounced the original proposal, saying it would not work. At hearings on the new rules, Dr. Young admitted that he had originally opposed the plan but that OMB officials, who have advocated less regulatory control, supported it.