In his first meeting with top executives from PepsiCo, W.K. Kellogg, General Mills and other large companies, Robert F. Kennedy Jr., the health secretary, bluntly told them that a top priority would be eliminating artificial dyes from the nation’s food supply.

At the Monday meeting, Mr. Kennedy emphasized that it was a “strong desire and urgent priority” of the new Trump administration to rid the food system of artificial colorings.

In addition, he warned the companies that they should anticipate significant change as a result of his quest for “getting the worst ingredients out” of food, according to a letter from the Consumer Brands Association, a trade group. The Times reviewed a copy that was sent to the group’s members after the meeting.

And while Mr. Kennedy said in the meeting that he wanted to work with the industry, he also “made clear his intention to take action unless the industry is willing to be proactive with solutions,” the association wrote.

“But to underscore, decision time is imminent,” Melissa Hockstad, who attended the meeting and is the group’s president, wrote in the letter.

Later on Monday, Mr. Kennedy issued a directive that would also affect food companies nationwide. He ordered the Food and Drug Administration to revise a longstanding policy that allowed companies — independent of any regulatory review — to decide that a new ingredient in the food supply was safe. Put in place decades ago, the policy was aimed at ingredients like vinegar or salt that are widely considered to be well-understood, and benign. But the designation, known as GRAS, or “generally recognized as safe,” has since grown to include a far broader array of natural and synthetic additives.

Mr. Kennedy had vowed to upend the food system as a way to address growing rates of chronic disease and other health concerns even before his appointment as the head of the Department of Health and Human Services. He now oversees the F.D.A., the federal regulator for about 80 percent of the nation’s food supply.

Many food companies rely on artificial dyes to make breakfast cereals and candies dazzling shades of pink and blue, for instance, or beverages neon orange. Some have already tried to adapt natural ingredients, like carrot or blueberry juice, for coloring, particularly for products sold in international markets, like Canada. But the companies have said that consumer demand had weakened in the United States because of dissatisfaction with less appealing or vivid colors in snacks and drinks.

Steven Williams, the chief executive of PepsiCo’s North America division, attended the meeting with Mr. Kennedy, but the company said he would not comment. In an email, a PepsiCo spokesperson said that the company viewed the meeting as a “productive first step” and added that it was focused on providing consumers “more options with natural ingredients, no synthetic colors and reductions in sugar, fat and sodium.”

Stacy Flathau, the chief corporate affairs officer for W.K. Kellogg, said in an emailed statement that the company looked forward to working with the new administration.

While the industry memo expressed alarm about the plan to remove synthetic colors, it did not address Mr. Kennedy’s additional proposal targeting some food ingredients deemed safe.

Advocates for food safety have criticized the existing GRAS policy as a loophole that enables food companies to introduce untested ingredients that in some cases have proven hazardous. About 1,000 ingredients deemed safe have been reviewed by the F.D.A., but Mr. Kennedy targeted the ones that companies deem acceptable with no government oversight.

“Eliminating this loophole will provide transparency to consumers, help get our nation’s food supply back on track by ensuring that ingredients being introduced into foods are safe, and ultimately Make America Healthy Again,” Mr. Kennedy said in a statement.

Bills to remove synthetic colors from the food supply have taken off since California banned Red Dye No. 3, a move that the F.D.A. followed. Other state proposals have targeted titanium dioxide, a compound used to make food appear shiny. Texas and West Virginia have moved to strip colorants from some school lunches.

In Ms. Hockstad’s letter to food company executives, she said Mr. Kennedy wanted synthetic color additives known as FD&C colors, or Food, Drug & Cosmetic dyes, removed during his administration.

Vani Hari, an activist known online as the Food Babe who did not attend the meeting, applauded Mr. Kennedy’s willingness to take on the food industry. “Bobby gave the food industry an ultimatum,” she said. “Either work with us to make these changes happen or we’ll do it ourselves.”

Mr. Kennedy was expected to meet with members of the Make America Healthy Again commission on Tuesday.

Stuart Pape, a lawyer who represents food companies, said Mr. Kennedy’s plan was “ambitious.” He said the F.D.A. traditionally had proposed removal of one coloring at a time, presenting research on why the ingredient was unsafe. Whether there is an adequate supply of alternative colorings would be a concern of a broader plan.

“I think Kennedy has made no secret that he intends to go after the food ingredients,” Mr. Pape said. “And I think this is the opening of that war.”

Dr. Peter Lurie, a former F.D.A. official and director of the Center for Science in the Public Interest, an advocacy group, said the effort might not have a significant effect on major chronic diseases including diabetes and heart disease.

The data on cancer related to food dyes was mostly focused on Red No. 3, he said. In the waning days of the Biden administration, the F.D.A. issued a ban on Red No. 3 that would take effect in the coming years. Red dye No. 3 has been linked to some cancers in animals, but not in humans.

Still, he said that Mr. Kennedy’s move might be effective because the dyes do little other than to make unhealthy food appear more appealing. Despite spending years fighting efforts to limit food dyes, he said, food executives may join other business leaders who have been eager to kowtow to the current administration.

“Given their fear of angering the administration,” Dr. Lurie said, “they may just see it in their interest to go along with this.”