Mr. Carr said that NPR and PBS stations operate as noncommercial broadcast organizations, but that they may be airing “announcements that cross the line into prohibited commercial advertisements.”

“To the extent that these taxpayer dollars are being used to support a for-profit endeavor or an entity that is airing commercial advertisements,” Mr. Carr wrote, “then that would further undermine any case for continuing to fund NPR and PBS with taxpayer dollars.”

The letter is the latest action from President Trump’s allies to target NPR and PBS stations and the Corporation for Public Broadcasting, a taxpayer-funded organization that backs them. Executives at NPR and PBS stations have been bracing for a potential battle over government funding, gaming out financial worst-case scenarios.