John Pistole, who oversees the air marshals as head of the Transportation Security Administration, said security had not been compromised by the behavior of some air marshals. "Absolutely not," Pistole told ABC News Tuesday. "The national security mission is always paramount."
"TSA took a proactive approach to the issues raised and has developed and implemented solutions ahead of the conclusion of the investigation," said the TSA in a statement to ABC News.
But some members of Congress questioned the report's conclusion that the mission was not compromised. The Inspector General's report also failed to fully investigate many of the more damning allegations made against air marshal managers.
"Our review does not support a finding of widespread discrimination and retaliation" within the Federal Air Marshal Service, the report said.
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.