About 315 scanners are currently in use at 65 US airports, according to the TSA, and the machines or body pat-downs are "the best technology we have today" to screen individuals, Pistole said.
He also brushed off health concerns that the equipment might expose people to dangerous levels of radiation.
Citing independent studies and research from the Food and Drug Administration (FDA), Pistole insisted going through scanners "is similar to receiving three minutes of radiation that you would receive on a normal (commercial) flight."
For people who may not wish to receive full-body pat-downs due to religious reasons, Pistole said: "While we respect that person's beliefs, (if they refuse the pat-down), they won't be getting on an airplane... no exceptions."
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