The US Federal Aviation Administration says it is the only authority that can suspend an airline from operating a specific route.
The clarification comes just days after the American Samoa governor, Togiola Tulafono, issued an executive order giving Hawaiian Airlines 90 days to leave American Samoa.
He claims that the carrier is charging unduly high fares and discriminates against Samoans.
But FAA spokesman, Allen Kenitzer, has told the Honolulu Advertiser newspaper that the FAA is the only government agency that can suspend flights.
Mr Kenitzer says such an order can only be made after the FAA demonstrates the legal grounds for action.