A former head of the Food and Drug Administration who led the charge against tobacco companies in the 1990s is aligning himself with Health Secretary Robert F. Kennedy Jr.’s war on ultraprocessed foods, offering a path to take on the industry while testing President Trump’s willingness to enter the fray.

In a citizen petition filed late Wednesday and shared with The New York Times, Dr. David Kessler, who held an advisory role in the Biden administration, argued that the agency he ran more than 30 years ago has the authority and the scientific evidence to declare that some of the core ingredients in ultraprocessed foods are no longer “generally recognized as safe.”

That includes sweeteners like high-fructose corn syrup and certain refined flours and starches like maltodextrin, dextrose and corn solids, which are used by the food industry but not in home cooking. A citizen petition is a formal request to the F.D.A.; the agency is obligated to respond in 180 days.

“This is the great public health challenge facing us,” Dr. Kessler said in an interview. “Twenty-five percent of American men are going to develop heart failure. Thirty to 40 percent of us are going to be diabetic. Twenty-five percent of us are going to have a stroke.”

“And the primary driver of that,” he added, “is our diet and what we are eating.”

The petition is both a gift and a shot across the bow to Mr. Kennedy, who has made no secret of his desire to restrict ultraprocessed foods, which account for more than half the American diet, and which he blames for the nation’s chronic disease epidemic.

Dr. Kessler is challenging the Trump administration to do what it has so far been unwilling to do: use government regulations to force the industry to change. So far, Mr. Kennedy’s major food initiative, removing artificial dyes from foods, has relied on the industry’s voluntary cooperation. The strategy outlined by Dr. Kessler, who ran the F.D.A. under presidents of both parties, would put Mr. Kennedy and Mr. Trump squarely at odds with interests that have traditionally backed Republicans.