Food and Drug Administration Commissioner Scott Gottlieb threatened Friday to pull e-cigarettes off the market if the agency's new restrictions on the sale of fruity flavors don't slow an "astonishing" surge in teen use.

"The reality is if we don't prevent this level of youth use of these products, this is an existential risk for the entire industry," Gottlieb said on CNBC's "Squawk Box." "The alternative is to pull the products off the market, which is not something we want to do."

Gottlieb rolled out new rules Thursday restricting sales of e-cigarette flavors, except for mint and menthol, mostly to vape shops and other stores that don't allow minors. The rules effectively ban most convenience stores and gas stations from selling the sweeter flavors, unless they segregate the flavors to a separate section of the store that prohibits minors.

E-cigarette companies who want to continue selling fruity flavors on their website must follow new FDA-mandated guidelines. Meanwhile, the agency will pursue bans on menthol cigarettes and flavored cigars.

E-cigarettes are billed as a way to give adult smokers their nicotine fix without all the toxins that come with conventional cigarettes. But many teens are also using these products now, throwing the industry's future into question.

"I think a lot of people are going to be willing to put up with a few inconveniences in order to really prevent these things from getting into the hands of kids," Gottlieb told CNBC.

Data from the Centers for Disease Control and Prevention's National Youth Tobacco Survey show 3.6 million middle and high school students currently use e-cigarettes, 1.5 million more than last year. Researchers suggest the popularity of "certain types of e-cigarettes, such as JUUL" likely caused the surge in e-cigarette use.

Gottlieb said these trends can't continue and if they do, he may take additional actions.

"There's no way to completely prevent access to kids, but we're going to put speed bumps to help prevent these things from getting into the hands of kids, particularly the fruity-flavored products," Gottlieb said.

E-cigarette manufacturers on Thursday said they planned to work with Gottlieb on his policies around e-cigarettes, although some implied they would fight a ban on menthol cigarettes. Health groups said Gottlieb didn't go far enough.

In September, Gottlieb ordered manufacturers to fix what he called "epidemic" levels of teens using e-cigarettes and specifically instructed five brands — Juul, British American Tobacco's Vuse, Altria's MarkTen, Imperial Brands' Blu E-cigs and Japan Tobacco's Logic — to submit plans detailing how they will prevent teens from using their products.

Juul, the clear e-cigarette market leader, on Tuesday stopped accepting retail orders for its mango, fruit, creme and cucumber pods from the more than 90,000 convenience stores, vape shops and other retailers that sell them, CEO Kevin Burns said Tuesday in a blog post on the company's website. Juul plans to resume sales to retailers that are legally allowed to sell flavored e-cigarettes and adopt the company's new age restrictions and verification system, though it's unclear when sales could resume.