"TSA took a proactive approach to the issues raised and has developed and implemented solutions ahead of the conclusion of the investigation," the TSA said in a statement in response to the ABC News report.
However other air marshals, still working undercover on flights and unable to reveal their names publicly, alleged that managers regularly scheduled themselves on flights so they could visit family or vacation spots.
In one example, the air marshals provided a photograph of a manager who arranged to fly to Brussels at Christmas time, and then jumped a fence to sit next to the Baby Jesus in a nativity crèche in the city's main square.
Former federal air marshal Theodoropoulos has had his own issues, stemming from an altercation with a bartender that led to his dismissal from the air marshals after a 20-year career in law enforcement.
He and his union say the government used a relatively minor incident as a way to get rid of a whistleblower and send a message to other air marshals to keep quiet.