"We don't know the longitudinal effect of these products," Merlo told CNBC's "Squawk Box." "Something has to be done."
In research released in October from New York University, scientists found e-cigarette vapor caused lung cancer, and potentially bladder cancer, in mice, and damaged their DNA, raising concerns about similar adverse effects in humans.
Flavored e-cigarettes have fueled what government regulators are calling a teen vaping epidemic, with data showing that more than 5 million U.S. teenagers are now vaping, with many preferring flavors.
Merlo said he saw signs that something was wrong with vaping in 2014, around the same time that CVS stopped selling tobacco products at its drug stores.
"I can remember going into a retail establishment that was selling [e-cigarettes] and I saw the device with the Hello Kitty logo and the bubblegum liquid," he recalled. "It absolutely raised the question of, 'wait a minute, what are we doing here?'"
The Trump administration in September said the administration was readying a ban on flavored e-cigarettes. However, Trump reportedly refused to sign off on the plan, under pressure from vaping advocates who contend that flavors help adults stop smoking regular cigarettes and that removing flavors would force vape shops around the country to close. As the White House mulls a decision, some state and city regulators have pushed legislation to ban all flavored e-cigarettes.
Ahead of any such action in Washington, market leading e-cigarette company Juul last month halted sales of its popular mint flavor, which accounts for the bulk of its U.S. revenue.
Banning flavors is a step in the right direction to stopping teen use, Merlo said. "We've made a lot of progress to create a tobacco-free generation," he added. "Vaping is taking us backwards."
Former FDA Commissioner Scott Gottlieb, who is also a CNBC contributor, told CNBC in November that Juul products should be removed from the market, citing two studies that showed the scope of teen use of its e-cigarettes and flavored pods.
Those studies published in the Journal of the American Medical Association found that Juul dominates the e-cigarette market among teens, with its mint pods being the most popular flavor. The studies also highlighted that 27.5% of high school students and 10.5% of eighth graders said they currently use e-cigarettes. More than half of both groups said they used Juul as their e-cigarette of choice.
In addition to the problem of teens using e-cigarettes, there's also the matter of the deadly vaping disease that's causing even more public alarm.