Speaking to reporters on the White House lawn, Mr. Azar said that removing flavor pods from stores just prompted youths to shift from fruit flavors to menthol and mint, which were still available, rather than to stop vaping altogether.

“What we’ve seen has been, and it may be connected, a huge spiking of children’s utilization of mint and menthol e-cigarettes, which remain, by all manufacturers, available in retail stores,” Mr. Azar said.

The issue appeared to hit home at the White House, where Melania Trump attended the meeting with Mr. Azar, Dr. Ned Sharpless, the acting F.D.A. commissioner and the president. “She’s got a son,” Mr. Trump said of their teenage child, Barron. “She feels very strongly about it,” he said.

Juul has repeatedly denied that it aimed its products at minors, but its sleek devices have become more and more popular and are easy to conceal. And even though the company’s array of flavors had disappeared from shelves, they were still available online, and a host of competitors sprouted up with lookalike versions and similar flavors to fill the vacuum. Juul had said that nearly 85 percent of its sales were from mint and other flavors, and that its decision to stop shipping them to stores had dented their sales.

On Monday, the F.D.A. took action against Juul, sending a warning letter accusing the company of violating federal regulations by promoting its vaping products as a healthier option than cigarettes.

As for the agency’s decision to prohibit most flavors, Ted Kwong, a Juul spokesman, said the company would comply. “We strongly agree with the need for aggressive category-wide action on flavored products,” he said.

Public health groups have long clamored for strict curbs on e-cigarettes and flavors, especially because they worried that the soaring use among youths was hooking a new generation on nicotine after decades of a decline in smoking rates.