Monday afternoon, John Pistole put out a public service announcement thanking travelers for their continued cooperation and to teach them about the new procedures.
"We appreciate your patience as we all work together to keep travel safe," Pistole says in the ad.
The move followed media appearances Monday morning.
Pistole assured "The Today Show" that he is hard at work to find the best balance between security and privacy.
"We're going to look at how can we do the most effective screening in the least invasive way, knowing that there's always a trade-off between security and privacy," Pistole said to Matt Lauer.
Pistole said that his job is to provide security, and he's doing everything he can to decrease potential travel threats.
"We just want to make sure that you and everybody else on that plane arrives safely," he said.
The new policy measures in question require passengers to go through a fully-body x-ray scan or submit to a "thorough" pat-down if that scan is refused.
These procedures were introduced following an incident from last Christmas in which a Nigerian traveler tried to ignite a bomb in his underwear in an attempt to take down a Detroit-bound plane. The incident is continuously referenced by Pistole.
Pistole said that of the 34 million people who've traveled since the new security measures were introduced, the number who've received the pat-down represents "a very small percent."
Pistole's interview reflected comments from a statement he released Sunday, in which he assured he constantly tries to strike the right balance between privacy and security.
"This has always been viewed as an evolving program that will be adapted as conditions warrant, and we greatly appreciate the cooperation and understanding of the American people," he said.
Pistole told CNN Monday morning that while the process is being reviewed, no changes will be made in the near future. But he does have a long-term plan, which includes speaking to the Government Accountability Office to determine if the screenings could be refined based on the information at hand.
"So we're looking at that and seeing if there's any basis or any way that we can modify yet provide that level of security that everybody wants," he said.
When appearing on "Face the Nation" Sunday morning, Secretary of State Hillary Clinton said that she understands how offensive the screening measures must be for the people who are going through them.
"Now, if there is a way to limit the number of people who are going to be put through surveillance, that is something that I am sure can be considered," she said. "But everybody is trying to do the right thing."