TSA Deputy Administrator John Halinski defended the agency's workforce, saying that employees who made mistakes were outliers.
"We screen approximately 600 million passengers a year," Halinski said. "We have engagement… with about 700,000 [passengers], about 8 percent are criticisms of TSA. I think that statistic speaks for itself."
Halinski said that TSA was "like a city" with a large population.
"You're always going to have crime in a city," he said. "You're always going to have people in a city who don't do things that are proper or make mistakes. I'm not saying we're any different than any group of Americans, I'm saying we're exactly like every group of Americans."
TSA says on its website that it has about 50,000 employees.
But Rogers said Wednesday that the agency's rules make it too difficult for bad employees to be disciplined or fired.
"One of my concerns all along with TSA has been when they have somebody that ... makes serious mistakes in judgement, they aren't terminated," he said. "They aren't really disciplined in a significant way. There have been some pretty egregious actions that if they were in the private sector, I think they would've been terminated."
Halinksi responded that TSA acts quickly to address problems with employee behavior.
"If any individual in TSA is identified as committing an act of theft, drugs — and we do test for drugs — or lack of screening ... if we can prove it immediately, we terminate the employee," he said.
Halinksi said that the media reports cited by Rogers were good because they were usually the result of TSA taking disciplinary action against an employee.
"We're policing our own," he said. "We are identifying problems, and we're conducting the appropriate action. In some cases it is terminating employees who have misconduct."
Halinski added that anonymous posts on the Internet have contributed to problems with TSA's reputation among airline passengers.
"It's very easy to put a negative comment in a blog and not put your name on it," he said.
Halinski added, however, that "when we see criticism, we're going to address criticism and we're going to address vulnerability."
Rogers said he was raising the issue because he was "concerned there might be some effort to inhibit your getting rid of bad apples, because the truth is the overwhelming majority of TSA employees and screeners are good employees, good people trying to do a good job."
"We can't let the whole organization be tainted by bad folks that you can't seem to get rid of," he said.