WASHINGTON — The Food and Drug Administration will create a senior position to oversee food safety and nutrition after recent foodborne-illness crises, including a baby formula shortage, exposed major flaws in the agency’s structure and culture.

The move is part of Commissioner Robert M. Califf’s reorganization of the FDA’s food policy apparatus. The agency’s duties are split between pharmaceuticals and medical devices on one side and food safety and nutrition on the other. But FDA leaders concede that its food responsibilities have received short shrift, leading to avoidable safety problems and long-running unresolved debates over nutritional and labeling requirements.

“You’ve ended up with a sort of jigsaw puzzle that doesn’t fit together,” Califf said in an interview. “What we’re doing here is creating a unified program that has clear lines of authority, clear lines of reporting, a concerted effort to create efficiency, the development of an enterprise-wide information technology system to support the operations and a single leader to whom it reports.”

Califf will appoint a deputy commissioner for human foods, he announced Tuesday, who will control an annual budget of close to $320 million and oversee the FDA’s Center for Food Safety and Applied Nutrition, as well as the Office of Food Policy and Response.

Crucially, though, the FDA’s high-powered Office of Regulatory Affairs – responsible for investigations, inspections, laboratory testing and import controls – will remain independent and serve functions across the FDA, including drugs and medical devices.

Some food safety advocates say that keeping regulatory affairs separate, along with the Center for Veterinary Medicine, which works closely with the human foods division, could significantly hinder the efficacy of a new food czar.

“If there’s this kind of dotted-line approach, that’s not really allowing the deputy commissioner to be effective,” said Brian Ronholm, director of food policy at Consumer Reports. “I think anyone who works in government can recognize that it’s direct-line authority that has the most impact in terms of where resources are directed. Anything short of that, it really runs the risk of almost reinforcing the current structural dynamics that caused the infant formula crisis.”

Califf’s moves come months after he asked a think tank, the Reagan-Udall Foundation, to evaluate the FDA’s food safety and nutrition programs. The agency was contending at the time with the infant formula crisis, in which allegedly tainted powdered formula was blamed for sickening four children and killing at least two.

A whistleblower complaint that flagged potentially catastrophic safety violations at an Abbott Laboratories formula factory in Sturgis, Mich., went unseen by the FDA’s top food safety official for months. Frank Yiannas, the deputy commissioner for the Office of Food Policy and Response, blamed long-lamented communication breakdowns for preventing the allegations from reaching his attention.

Yiannas announced his resignation last week. In a letter to Califf, he said organizational flaws “significantly impaired FDA’s ability to operate as an integrated food team and protect the public.”

The formula crisis and shortage, which persists in some parts of the country, triggered congressional hearings and calls to break up the FDA into separate agencies within the Department of Health and Human Services: one focused on food and nutrition and another on drug and medical-device approvals and safety.

The Reagan-Udall Foundation recommended that approach, arguing that it would elevate the visibility of the food program and provide it with its own budget. About $1.1 billion – or 18 percent – of the FDA’s $6.1 billion budget in 2021 was spent on its food program, according to the nonpartisan Congressional Research Service.

Of that amount, the Reagan-Udall Foundation reported, $722.2 million was spent on regulatory affairs, a department whose duty spans not only food programs, but medical devices and drugs and veterinary medicine.

Califf would not endorse splitting up the FDA, which would require congressional approval, but said it “deserves some due consideration.”

“Food is not just about safety; medical products are not just about safety,” he said. “They’re also about, on the food side, nutrition. And on the medical product side, it’s about efficacy, and the balance of benefits and risks.”

Janet Woodcock, the FDA’s principal deputy commissioner, said dividing the FDA risked creating two small agencies that would compete for resources and struggle to achieve their missions.

“I don’t see how that’s really a fix,” Woodcock said.

But some food safety advocates say that Califf’s restructuring does not go far enough. Bill Marler, a high-profile food safety attorney, said the commissioner’s moves “just rearrange the deck chairs.”

A consortium of consumer rights and industry groups called on Califf to unite regulatory and veterinary components under the new food deputy commissioner, saying it would be “foundational to its operational success and essential culture change.”

The Reagan-Udall report said the FDA’s food program had “a culture of indecisiveness and inaction and created disincentives for collaboration.”

“Now is the time for real reform at FDA,” Sen. Dick Durbin, D-Ill., and Rep. Rosa DeLauro, D-Conn., wrote in a letter to Califf on Monday. “It is not the time for half measures or more excuses.”