"It is a source of continual astonishment to me that pilots -- many of whom, it should be pointed out, are military veterans who possess security clearances -- are not allowed to carry onboard their airplanes pocket knives and bottles of shampoo, but then they're allowed to fly enormous, fuel-laden, missile-like objects over American cities," he added.
Captain Mike Cleary, head of the US Airways Pilots Association, followed up saying the new searches are "intrusive and have been implemented almost overnight" and that one pilot was so traumatized that he couldn't do his job.
"The words this pilot used to describe the incident included 'sexual molestation,' and in the aftermath of trying to recover, this pilot reported that he had literally vomited in his own driveway while contemplating going back to work and facing the possibility of a similar encounter with the TSA," Cleary said.
Cleary advised pilots to have a fellow crew member on hand to witness a patdown.
But at least one security expert says this is just politicking by pilots who want their own pass through security and that such invasive searches are necessary.
"If you don't do an invasive patdown, you can miss something. Of all people, the pilots should understand that," said Douglas R. Laird, a former director of security at Northwest Airlines who now runs his own aviation security consulting company Laird & Associates, Inc. "I think they are playing politics."
Napolitano said that she recognized that the pilots had concerns, especially when they are the trusted individuals who ensure the safety of passengers once they are on the planes.
"Now the pilots have raised some objections, part of it is because they have to go through so many times -- it's not about radiation I think so much as, 'look, we're pilots, we control the planes anyway.'" Napolitano said, "They would like to have some kind of expedited way to get through security, recognizing they're actually going to be in the cockpit. And, you know they have a legitimate argument there. We recognize that, we're working with the pilots groups and we hope to very quickly be able to announce some things where pilots are concerned."
Laird flew out of airports in Denver and Los Angeles last week and watched screeners do the new patdowns. Yes, he said, they are very invasive but necessary.
"If you don't get up and really feel to make sure that there's nothing there, there's no point in doing it," he said. "For men and women both, you have to feel the crotch area to make sure there is nothing there. The only way to do that is to be intrusive."
He blames the TSA for doing a poor job of explaining the new searches to the public.
"The dilemma they are in is if they explain too much, they risk scaring the public," he added. "I think it's a small liberty to give up for the safety of all."
With reports from ABC News Jason Ryan