Since taking office in February, Health Secretary Robert F. Kennedy Jr. has put an unmistakable stamp on American vaccine policy.

He has effectively restricted access to Covid shots, installed skeptics to influential posts and ousted the director of the Centers for Disease Control and Prevention after she defied his orders on inoculations.

But Mr. Kennedy has applied a far lighter touch to what he and his Make America Healthy Again movement have described as the other major scourge plaguing American children: pesticides and unhealthy foods.

Far from cracking down on food and farming practices, Mr. Kennedy’s MAHA commission report on Tuesday defended existing pesticide review procedures and, in some cases, called for loosening food regulations, even as the report promised future steps to clean up what children eat.

To many scientists — and some of Mr. Kennedy’s own followers — the gap between the health secretary’s use of his authority over food quality and his pummeling of vaccines has created a jarring split screen.

“It seems like the vaccine issues were very much like, ‘Go ahead, Bobby, here’s your green light, do what you want,’” said Elizabeth Frost, a MAHA organizer in Ohio. “It feels like it’s a very different conversation and a very different environment around pesticides and food.”

Mr. Kennedy’s restraint in using the levers of government on those parts of the MAHA agenda has dismayed some supporters, threatening to fracture the uneasy alliance between the movement’s anti-chemical activists and Republican lawmakers who see themselves as champions of the agriculture industry.

At the same time, scientists sympathetic to the health secretary’s ideas about cleaning up the food supply worry that he has diluted measures long backed by studies, even as he works aggressively toward a separate goal — undercutting vaccines — that defies decades of research.

“In the vaccine world, he’s forcing change, and I would say that when it comes to food and nutrition, it’s really been all talk,” said Lindsey Smith Taillie, a nutrition epidemiologist at the University of North Carolina at Chapel Hill.

“MAHA has talked a big game about wanting to end chronic disease through better diet and physical activity, but has so far been unwilling to implement the kind of meaningful policy change required to do that,” she said.

In campaigning for President Trump last year, Mr. Kennedy described protecting Americans from pesticides as a main reason for the pair’s growing bond. At an August 2024 rally in Glendale, Ariz. after he endorsed Mr. Trump, Mr. Kennedy never mentioned vaccines.

He instead emphasized their shared commitment to safe food. Mr. Trump agreed. “Millions and millions of Americans who want clean air, clean water and a healthy nation have concerns about toxins in our environment and pesticides in our food,” Mr. Trump said.

Days before the election, Mr. Kennedy went further, pledging that if he were chosen to serve in a second Trump administration, he would “ban the worst agricultural chemicals that are already prohibited in other countries.”

His early actions as health secretary heartened MAHA supporters. Food companies volunteered to phase out several artificial food dyes in the coming years, a response to calls from Mr. Kennedy and the cultural reckoning he had forced into view.

The health secretary took his campaign for clean food to the states, standing beside Republican lawmakers in the spring to celebrate state laws banning certain food dyes — laws that had once appealed largely to Democratic legislators.

And the Trump administration granted waivers to some states restricting recipients of federal food assistance from using their benefits to buy junk food.

“That is something that no prior administration has been able to do,” said Alyssa Moran, a nutrition policy expert at the University of Pennsylvania. “And it really is taking on Big Soda.”

But a MAHA movement that Mr. Kennedy once said would bring about a clampdown on toxins in the food and soil has recently run headlong into the deregulatory agenda of other segments of the Republican coalition.

The Environmental Protection Agency has weakened limits on certain environmental pollutants, including mercury, whose dangers Mr. Kennedy has inveighed against for years.

Instead, House Republicans have pushed measures that would grant liability relief to pesticide companies and constrain E.P.A. regulation of so-called forever chemicals.

The latest MAHA commission report represented the Trump administration’s most public attempt to resolve the tension between a MAHA movement bent on restricting certain foods and chemicals and Republican lawmakers allied with the very industries behind those products.

The report did say that the Food and Drug Administration would close a loophole that allows companies to add substances to the food supply without informing the agency, a step that Dr. Moran said nutrition activists have sought for years.

And on a separate front, Mr. Trump directed his administration later Tuesday to revive a decades-old policy that would restrict advertising of prescription drugs on television.

In an interview, Calley Means, a close adviser to Mr. Kennedy, said the administration was moving “as fast as humanly possible” to enact reforms and update the nation’s dietary guidelines, even as he said that compromises were inevitable.

“In the first year of the Trump administration, the federal government will enact more food policy reform than at any time in modern American history,” he said.

Mr. Means added: “Secretary Kennedy and many in the MAHA movement have transitioned from advocates to controlling levers of power at the federal government. The U.S. democratic system involves compromise balancing American health, the American economy, American innovation, many complicated factors.”

To the chagrin of some who were partial to the food and pesticide measures that Mr. Kennedy backed as an advocate, the report on Tuesday did not propose bans on pesticides. It offered no clear timeline for reducing the country’s reliance on ultraprocessed foods. It steered clear of other regulations, like taxes on sugary drinks.

And calls for revisions to nutrition labels and limits on the marketing of unhealthy food to children were thin on details about how such programs would be funded or implemented.

The idea that inducing food makers to swap artificial dyes for natural dyes would itself make food healthy was far-fetched, scientists said. Marion Nestle, a professor emerita of nutrition, food studies and public health at New York University, said the evidence on color additives was “very mixed and weak” in the first place.

And rather than restricting school sales of beverages like flavored milk that have added sugar, the report instead proposed opening the door to more whole milk in schools, a far lower priority for nutrition scientists. That proposal appeared in a section titled “food deregulation.”

Dr. Taillie said, “Usually when you see something like that, it speaks to industry lobbying.”

The health secretary’s allies also noticed.

David Murphy, a former finance director for Mr. Kennedy’s presidential campaign, called the report a “clear sign that Big Ag, Bayer and the pesticide industry are firmly embedded in the White House.”

The report’s promise to make the public aware of what it described as “robust review procedures” governing pesticide use was “a pathetic attempt to assuage the American people,” said Zen Honeycutt, the founder of Moms Across America, a group closely linked to the MAHA movement.

Jillian Michaels, a fitness trainer best known for her work on “The Biggest Loser” and an influential voice in MAHA circles, said in an interview that she was shocked the Trump administration had taken such significant steps on vaccines, like canceling federal money for developing mRNA shots.

“Any win is a win,” she said. “I can’t believe when there is one.”

But when it comes to “the 50,000 chemicals you’re coming into contact with every single day that you and I aren’t even aware of,” Ms. Michaels said, people could only do so much on their own. “You need some regulatory help, period,” she said.

“Baby steps,” she added. “You’ve got to be patient.”

As health secretary, Mr. Kennedy has power over vaccines that he does not over pollutants or farming practices, which are the responsibility of the E.P.A. and the Department of Agriculture.

Mr. Kennedy has also surrounded himself with unconventional advisers, leaving the health department without the types of seasoned regulators and rule makers who might have been more adept at turning his anti-chemical campaign into government action, analysts said.

“To put the best possible face on it, he’s been outmaneuvered,” said Ken Cook, the president of the Environmental Working Group, which has fought for state regulations on food chemicals.

The health secretary deserved credit for backing those state measures, Mr. Cook said. But, he added, “We’ve had to resort to this piecemeal state-by-state thing because the federal government wasn’t doing its job.”

He added: “Now you’re there, Bobby. You could do it.”

The rollout on Tuesday of the MAHA commission report offered a vivid illustration of the health secretary’s caginess on the causes that once powered his own presidential campaign.

Asked by a reporter about pesticides, Mr. Kennedy demurred.

“You want to answer, Lee, or … ” the health secretary said, trailing off.

He was referring to Lee Zeldin, the E.P.A. administrator, whose agency has not only relaxed standards for mercury pollution but also delayed the implementation of Biden-era regulations of dangerous chemicals.

Mr. Kennedy’s cabinet colleagues went on to praise the government’s existing pesticide review process.

By contrast, the health secretary was unbridled in talking about plans to investigate the dangers of vaccines. Asked about the report’s promise that the government would strengthen oversight of vaccine injuries, Mr. Kennedy gave a three-and-a-half-minute answer.

“We’re changing the system,” he said. “We are recasting the entire program.”