A sign directs travelers to a security checkpoint staffed by Transportation Security Administration workers at O'Hare Airport on June 2, 2015 in Chicago.
Washington CNN  — 

The administrator of the Transportation Security Administration defended his agency Thursday in testimony before the House Oversight Committee over accusations of mismanagement, retaliation against whistleblowers and complaints of longer security lines.

Committee members focused on the TSA’s reported practice of directed reassignments, where employees who have highlighted wrongdoing within the administration are shifted to other assignments. The committee said some of those reassignments amount to punishment and cost the agency millions of dollars.

The charges of reassigning whistleblowers comes on the heels of testimony by three former TSA employees who reported that they were retaliated against. Last month, a TSA employee at Minneapolis-Saint Paul International Airport alleged in testimony before Congress that he was instructed to racially profile Somali-Americans.

“That testimony is very troubling to me, because what I’m not going to tolerate is retaliation on whistleblowers and that’s what it looks like to me,” Rep. Mark Meadows, R-North Carolina, told TSA Administrator Peter Neffenger.

“I don’t tolerate it either,” Neffenger replied. “If, in fact, there is retaliation, I will look into it.”

Arizona Republican Rep. Paul Gosar asked, “In your opinion, was this (reassigning whistleblowers) an appropriate use of directed reassignment, and if so, what’s your justification?”

Neffenger replied, “In my opinion, it was not an appropriate use of directed reassignments and that’s why I changed the policy.”

And while the committee said not only are employees uncovering misconduct retaliated against, some senior officials with poor performance records were given large bonuses and awards which damage “morale agency-wide.”

Neffenger attributed the long lines to the thousands of employees the administration lost in 2014 that they have yet to replace. But much harder to explain was the $90,000 bonus given to Kelly Hoggan, assistant administrator for the Office of Security Operations at TSA, following a scathing report by Department of Homeland Security Inspector General John Roth that detailed numerous security failures at airports around the country.

Additionally, the bonus paid to Hoggan was doled out in $10,000 increments, leading the committee to believe that the TSA was attempting to be less than transparent, accusing the administration of “smurfing” the payment.

“When I came into this organization last year, I found an organization with 5,800 fewer screeners and it had fewer front-line officers than it had four years previously,” Neffenger said. “And that was in the face of significantly higher traffic volume.”

In regards to the punishment of whistleblowers and the rewarding of poor performances, Neffenger told the committee that although he was not in charge of the TSA when Hoggan’s bonus and others were paid, he’s taken precautions to ensure the practice does not continue.