After more than three years of debate, the Reagan administration proposed new rules yesterday that would allow the nation's food companies to proclaim the health advantages of their products on labels and packaging.

The proposal would reverse a federal policy in effect since 1906 against advertising health claims for foods. Officials of the food industry, who have been eager to take advantage of America's increasing appetite for healthy foods, have pushed hard for the rule change.

Consumer groups have also sought labeling with more nutritional information, but spokesmen for the groups said the proposed change, published in yesterday's Federal Register, would allow food companies to tell only the most favorable part of the story.

"This is an open invitation to mislead the consumer," said Dr. Sidney Wolfe, director of the Public Citizen Health Research Group. "The companies get the best of all worlds. They can accentuate the postive and eliminate the negative."

The rule would prevent companies from placing unproven nutritional information or claims that a product cures a disease on any label. But it would permit packaging to link products and specific health benefits without having to refer to possible drawbacks.

In announcing the proposed change, for instance, Health and Human Services Secretary Otis R. Bowen mentioned milk as a prime candidate for new labeling.

"An example might be 'Milk products are good sources of calcium, which is important in a balanced diet for strong bones,' " he said.

But critics of the proposal said that type of label would give the consumer an improper sense of the overall benefits of milk in the average diet.

"Milk not only has calcium but lots of animal fat," said Bruce Silverglade, director of legal affairs for the Center for Science in the Public Interest. "Too much fat is a much bigger problem for the vast majority of American diets than a lack of calcium."

Bowen said the Food and Drug Administration, the Department of Agriculture and representatives of the Public Health Service will establish a committee to develop new health messages for use on food labels. He said the Federal Trade Commission, which monitors truth in advertising, will participate in the committee meetings.

The published regulations give far more latitude to the food industry than did earlier drafts. The first draft, for example, suggested that any label information "should be of a type that assists the consumer to develop a sound total dietary pattern that will enhance his or her health."

Yesterday's proposal says information on labels must be truthful and that information on food labels must never distort the role of that product in enhancing good health.

"This is a tricky situation," said Edward Scarbrough, deputy director of the FDA's office of nutrition and food science, who helped write the regulations. "The fundamental problem is and always has been how do you allow appropriate messages to be printed without opening up Pandora's box."

He said that before 1906, when food companies could make any claim they wanted for their products, many items were sold under blatantly false advertising.

"Soft drinks came onto the market not as foods, but as digestives that helped soothe the aching stomach," he said. "Often, they did no such thing."

Much of the movement for stronger links between health claims and nutritional information began in 1984, when Kellogg Co. launched a major promotional campaign by stating on the back panel of its All-Bran cereal the role of high-fiber diets in reducing the risk of cancer.

The campaign caused intense debate at FDA and within the industry. Although the National Cancer Institute also advertised fiber as beneficial in reducing cancer risk, the federal government did not want to open the way to claims that were less reputable.

"Americans are becoming more educated about their diets and the connection between food and health," said Ellen Morton, a spokeswoman for the National Food Processors Association, which represents major food companies and industry suppliers. "This will help them. A lot of money goes into marketing and advertising at food companies."