Mindful of the criticisms of the agency, Peter V. Neffenger, a former Coast Guard admiral who was appointed administrator last year, moved quickly to start a program to train all workers to better detect weapons, and called for more aggressive policing by airports’ oversight of security badges.

Last month, the T.S.A. announced a change in its policy of involuntarily reassigning senior staff members to other airports, a practice that many workers say had been used to punish workers who spoke out by sending them to undesirable locations.

John S. Pistole, a former administrator of the T.S.A. who created the Office of Professional Responsibility to establish uniform discipline and punishment across the agency, said claims by agency whistle-blowers were disconcerting, if true.

“There should never be any retaliation against workers for reporting a security violation,” he said. “This was not the standard I had for supervisors.”

Even those workers who were reinstated after their complaints were found to have merit have had to spend thousands of dollars fighting the T.S.A. in court or in complaints before whistle-blower agencies, resulting in a chilling effect.

“These workers look around and see what’s happening with those who report security violations, and remain silent because they have kids to feed and a mortgage to pay,” said Robert J. MacLean, a federal air marshal who last year won a case against the agency for wrongful firing that went all the way to the Supreme Court.

Files from whistle-blower protection agencies and the E.E.O.C. show numerous examples of retaliation by the T.S.A. against workers reporting misconduct and security violations.