Chief Privacy Officer Damien Kieran and Chief Compliance Officer Marianne Fogarty have also resigned, according to an internal message seen by Reuters.
He announced plans to cut half its workforce last week, promised to stop fake accounts and is charging $8 a month for the Twitter Blue service that will include a blue check verification.
"We are tracking recent developments at Twitter with deep concern," Douglas Farrar, the FTC's director of public affairs, told Reuters.
"Elon puts rockets into space, he's not afraid of the FTC," the attorney quoted Spiro as saying.
Twitter did not respond to a request for comment on the FTC warning, the note from the attorney or the departures.