The Food and Drug Administration on Thursday proposed measures that would all but eliminate artificial trans fats — the artery-clogging substance that is a major contributor to heart disease in the United States — from the food supply.

Under the proposal, which is open for public comment for 60 days, the agency would declare that partially hydrogenated oils, the source of trans fats, were no longer “generally recognized as safe,” a legal category that permits the use of salt and caffeine, for example.

That means companies would have to prove scientifically that partially hydrogenated oils are safe to eat, a very high hurdle given that scientific literature overwhelmingly shows the contrary. The Institute of Medicine has concluded that there is no safe level for consumption of artificial trans fats.

“That will make it a challenge, to be honest,” said Michael Taylor, deputy commissioner for foods at the FDA.

Dr. Margaret Hamburg, the agency’s commissioner, said the rules could prevent 20,000 heart attacks and 7,000 deaths from heart disease each year.

The move concluded three decades of battles by public health advocates against artificial trans fats, which occur when liquid oil is treated with hydrogen gas and made solid. The long-lasting fats became popular in frying and baking and in household items like margarine, and were cheaper than animal fat, like butter.

But over the years, scientific evidence has shown they are worse than any other fat for health because they raise the levels of so-called bad cholesterol and can lower the levels of good cholesterol. In 2006, an FDA rule went into effect requiring that artificial trans fats be listed on food labels, a shift that prompted many large producers to eliminate them. A year earlier, New York City told restaurants to stop using artificial trans fats in cooking. Many major chains like McDonald’s, found substitutes and eliminated trans fats.

Healthier people

Those actions led to major advances in public health: Trans fat intake declined among Americans to about one gram a day in 2012, down from 4.6 grams in 2006. A report from the Centers for Disease Control and Prevention found that blood levels of trans fatty acids among white adults in the United States declined by 58 percent from 2000 to 2009.

But the fats were not banned, and still lurk in many popular processed foods, such as microwave popcorn, certain desserts, frozen pizzas, margarines and coffee creamers.

“The artery is still half clogged,” said Dr. Thomas Frieden, the director of the disease centers. “This is about preventing people from being exposed to a harmful chemical that most of the time they didn’t even know was there.”

On the label

Frieden noted that artificial trans fats are required to be on the label only if there is more than half a gram per serving, a trace amount that can add up fast and lead to increased risk of heart attack. Even as little as 2 or 3 grams of trans fat a day can increase the health risk, scientists say.

“It’s quite important,” said Frieden, who led the charge against the fats in New York when he was health commissioner there. “It’s going to save a huge amount in health care costs and will mean fewer heart attacks.”

Some trans fats occur naturally. The FDA proposal only applies to those that are added to foods.

Public health advocates applauded the measure.

“Most of it is gone, but what remains is still a serious problem,” said Michael Jacobson, executive director of the Center for Science in the Public Interest, which petitioned the FDA to require artificial trans fats to be listed on nutrition labels as early as 1994.

“I suspect there are thousands of smaller restaurants that continue to use it out of ignorance,” he said, adding that they ask: “‘Trans what?’ They just use whatever the supplier sends.”

But public awareness can be powerful. This summer Jacobson’s nonprofit group drew attention to the fact that the so-called Big Catch fried fish meal at Long John Silvers, which comes with fried hush puppies and fried potatoes, contained 33 grams of trans fat. The restaurant chain has since promised to eliminate trans fats by the end of the year.

Phasing them out

The agency isn’t yet setting a timeline for the phase-out. Different foods may have different timelines, depending how easy it is to find a substitute.

“We want to do it in a way that doesn’t unduly disrupt markets,” Taylor said. Still, he says, the food “industry has demonstrated that it is, by and large, feasible to do.”

To phase them out, the FDA said it had made a preliminary determination that trans fats no longer fall in the agency’s “generally recognized as safe” category, which is reserved for thousands of additives that manufacturers can add to foods without FDA review. Once trans fats are off the list, anyone who wants to use them would have to petition the agency for a regulation allowing it, and that would likely not be approved.

Dr. Leon Bruner, chief scientist at the Grocery Manufacturers Association, said in a statement his group estimates that food manufacturers have voluntarily lowered the amount of trans fats in food products by 73 percent.

The group, which represents the country’s largest food companies, did not speculate on a reasonable timeline or speak to how difficult the move may be for some manufacturers. Bruner said in a statement that “consumers can be confident that their food is safe, and we look forward to working with the FDA to better understand their concerns and how our industry can better serve consumers.”

FDA officials say they have been working on trans fat issues for around 15 years — the first goal was to label them — and have been collecting data to justify a possible phase-out since just after President Barack Obama came into office in 2009.

The Center for Science in the Public Interest first petitioned FDA to ban trans fats nine years ago. Jacobson, the group’s director, says the move is “one of the most important lifesaving actions the FDA could take.”

He says the agency should try to move quickly as it determines a timeline. “Six months or a year should be more than enough time, especially considering that companies have had a decade to figure out what to do,” Jacobson said.