Mr Trump told reporters vaping was a "new problem", especially for children.
US Health Secretary Alex Azar said the Food and Drug Administration (FDA) would finalize a plan to take all non-tobacco flavors off the market.
Joining Mr Trump at the White House on Wednesday, Mr Azar said it would take the FDA several weeks to distribute the new guidance on e-cigarettes.
Mr Trump told reporters his administration would implement strong rules to protect "innocent children".
"We can't allow people to get sick and we can't have our youth be so affected," he said, adding that he hopes today's announcement will lead to parents becoming "tougher".
"People are going to watch what we're saying and parents are going be a lot tougher with respect to their children.
"A lot of people think vaping is wonderful, it's great. It's really not wonderful."