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. 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. 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.