"We are going to have to do something about it," Trump said after a meeting with health policy advisers, describing vaping as a "new problem in the country."
The Food and Drug Administration will soon issue guidance on how to take flavored vaping products off the market, said Health and Human Services Secretary Alex Azar, a process that could take months.
These products are currently sold under an FDA waiver.
It's unclear whether vaping companies could take legal action to block a ban.
Members of Congress have also discussed taking action amid concern about the physical effects of e-cigarettes. The Centers for Disease Control and Prevention is investigating more than 450 cases of lung disease that some officials believe were triggered by vaping.
At least six deaths have been attributed to the mysterious lung disease.
Two days ago, first lady Melania Trump expressed concern about "the growing epidemic" of e-cigarette use by children. She tweeted, "we need to do all we can to protect the public from tobacco-related disease and death, and prevent e-cigarettes from becoming an on-ramp to nicotine addiction for a generation of youth."
Melania Trump and vaping:: first lady tweets she is ‘deeply concerned’ about youth vaping
This article originally appeared on USA TODAY: Donald Trump moves to ban flavored vapes, targets e-cigarettes