But he said they are necessary for the "best security possible."
Pistole said he and other high-ranking officials at the Department of Homeland Security underwent the modern pat-downs before making them mandatory nationwide.
The pat-down "was more invasive than what I was used to. Of course, what is in my mind, from almost 27 years with the FBI and all of the counter-terrorism work since 9/11 is what are the plots out there, and how are we informed by the latest intelligence and the latest technology, and what do we need to do to assure the American people that, as they travel, that we are being thorough."
Pistole cited the attempted Christmas Day bombing on an airliner headed for Detroit by a suspect allegedly hiding explosives under his clothes.
"I am very sensitive to and concerned about people's privacy concerns, and I want to work through that as best we can," Pistole said. But the "bottom line is we need to provide for the best possible security."
As for privacy complaints about full-body scanners, Pistole said "the officer who sees the image never sees the person. The officer who sees the person never sees the image. And the machines are specifically disabled ... in terms of any retention, storage or ability to transmit those images."
He said the next generation of scanners will have "a stick figure, or a blob, if you will -- two options," instead of someone's exposed body.
Pistole testified before the Senate Committee on Commerce, Science and Transportation before the brouhaha erupted over the agency's full-body scans and pat-downs, CNN reported.
Protesters said the scans are invasive and amount to a virtual strip search.
US Airways pilot Capt. Chesley Sullenberger, who landed a crippled aircraft on the Hudson River last year, joined the opposition to the heightened airport security procedures, saying using full-body pat-downs and advanced scanners for airline personnel "just isn't an efficient use of our resources," CNN said.
"We're among the most scrutinized professional groups in the country, even more than doctors," Sullenberger said, suggesting flight crews should be allowed to bypass much of the security screening required of passengers.
The TSA said in a statement it can use "professional discretion" to determine whether individuals should be subject to further screening.
At least two lawsuits challenging the full-body imaging on health and privacy grounds have been filed.