Regulators are considering prohibiting some e-cigarette sales in convenience stores and confining them to vape shops, Food and Drug Administration Commissioner Scott Gottlieb told CNBC on Friday.

High school e-cigarette use surged 77 percent last year, Gottlieb said in an interview on "Squawk Box," citing preliminary figures from the federal Youth Tobacco Survey. Middle school use skyrocketed about 50 percent last year, he said. Gottlieb has called these levels "epidemic."

Many teens are illegally buying e-cigarettes, including the most popular one, Juul, in convenience stores, Gottlieb said. To confront the issue, he said, regulators could limit sales of flavored e-cigarette products to vape shops.

"We're looking at what can be sold in brick-and-mortar stores and whether or not flavored products can be sold in regular stores like a 7-Eleven and a truck stop and a gas station, or whether or not flavored products on the market should be confined to adult vaping shops, which generally tend to do a better job of checking ID," Gottlieb said.

The agency conducted a retail blitz over the summer, the largest coordinated enforcement effort in FDA history, and issued more than 1,300 warning letters and fines to retailers who illegally sold Juul and other e-cigarettes to minors.

Retailers who were caught include national convenience stores and gas stations like 7-Eleven, Circle K, Shell and Mobil, according to an FDA database.

The FDA is also weighing a ban of online sales of e-cigarettes while it crafts regulation with guidelines on online sales, he said.

These moves are part of the FDA's crackdown against youth e-cigarette use. Last month, the agency ordered five manufacturers — Juul, British American Tobacco's Vuse, Altria's MarkTen. Imperial Brands' Blu E-cigs and Japan Tobacco's Logic — to submit plans to address teen use of their products within 60 days.

Gottlieb said Friday the FDA has now met with Juul, Altria and Reynolds, a unit of British American Tobacco.