"I think TSA is on a good, upward trajectory," Neffenger said in an interview earlier today with ABC News' David Kerley.
During the Spring Break travel period, travelers faced hours-long security lines, causing many people to miss their flights. Frustration toward the TSA grew exponentially.
"We simply didn't have the number of people we needed for the volume of passengers," Neffenger explained.
In response to the long wait times, Neffenger said his agency has made significant changes to address fliers' complaints.
"We brought on about just shy of 1,400 new transportation security officers this summer, we converted about 2,000 [employees] from part-time to full-time, [and] we've added about another 50 or 60 canines which allow us to rapidly move people through the line," Neffenger said in the interview.
Neffenger explained that the agency also increased its ability to reach its customers, using social media like Twitter and Facebook to work with travelers that encounter problems on their journeys. Anecdotally, the response to the new workforce has been mostly positive, Neffenger said.
"We get criticism as well, but we're able to actually act on it very quickly now, where the goal is about a 15 minute turnaround when somebody writes to us," said Neffenger.
He added: "No security system will ever be a 100 percent acceptable to everybody that goes through, but the goal is to reduce the tension, reduce the friction to the traveler, and to try to make it at least as pleasant an experience as it can be, given that we have to screen people to make the system safe."
Kerley asked Neffenger what travelers can expect in the coming months and years.
TSA will also look at expanding its use of biometrics.
"To the extent that you're willing to provide additional information about yourself and biometrics, technology right now would allow us to expedite you through even better, ultimately removing the need to do document checks for people who are already in the system," Neffenger said. Passengers can opt out of the program, he added.
How will a new White House administration impact the TSA?
"We're looking forward to ensuring a smooth transition to the incoming administration. We've got a lot of issues to work with... [but] we're going to make sure there's no reduction in transportation security as we move through the next few months," he noted.
ABC News' Thomas Thornton contributed to this report.