WASHINGTON — The Supreme Court on Wednesday handed a win to the Food and Drug Administration over its refusal to approve flavored e-cigarettes.

The court threw out an appeals court ruling that found the agency unlawfully changed the rules in the middle of proceedings when it was deciding whether to approve various products.

With e-cigarettes, or vapes, more popular than ever, the case put the FDA’s role in the approval process under scrutiny. Despite the agency’s refusal to approve many products, flavored vapes have remained widely available.

Writing for a unanimous court, conservative Justice Samuel Alito stopped short of ruling definitively that the FDA had acted unlawfully on one particular aspect of the case: whether the agency should have considered the companies’ marketing plans as part of the approval process.

That issue will now be decided by the lower court.

But Alito said that the FDA’s decisions were otherwise sound, noting that the companies’ own applications are “strong evidence that regulated entities had adequate notice of the sort of comparative analysis the FDA anticipated.”

The FDA, then under the Biden administration, appealed to the Supreme Court after the New Orleans-based 5th U.S. Circuit Court of Appeals ruled that it had incorrectly handled the approval requests made by manufacturers, thereby violating the federal Administrative Procedure Act.

The agency has won similar cases in other courts.

Triton Distribution, which makes e-liquids for vape pens with flavors like Signature Series Mom’s Pistachio and Suicide Bunny Mother’s Milk and Cookies, is one of the companies involved. The other is Vapestasia, which has sought approval for Iced Pineapple Express, Killer Kustard Blueberry and other flavors.

The FDA has said flavored vapes pose a health risk because they could encourage young people to use tobacco.

The companies could face potential civil and criminal penalties for marketing products without approval. They argued the FDA got it wrong in denying the approvals, saying that flavored vapes can be used to help people stop smoking.

Their lawyers said the FDA changed its standard for considering flavored vapes in the middle of the process without giving applicants adequate warning.

The agency responded in court that it evaluates each application on its merits and that the companies had failed to provide sufficient evidence for their claims.

The FDA began regulating vape products in 2016 after they were already on the market. At the time, the agency said it would not take enforcement actions while companies sought approval.

It subsequently concluded that the potential benefits of helping adult smokers quit do not outweigh the potential health risks to young people, who are most attracted to nontobacco-flavored vapes.

The FDA has given its approval to menthol-flavored e-cigarettes, as well as some that are tobacco-flavored.