While some travelers do not like them, Napolitano in an interview broadcast Sunday insisted the practices will not change for the "foreseeable future."
The new technology and the pat-downs are "objectively safer for our traveling public," said Napolitano, adding she's always looking to improve the security systems in place.
Napolitano also dismissed a recent news report about major airports failing secrets tests designed to get contraband such as guns and knives past security screeners. The report said some airports had a 70 percent failure rate.
"Many of them are very old and out of date and there were all kinds of methodology issues with them. Let's set those aside," she said on "State of the Union" on CNN. "We pick up more contraband with the new procedures and the new machinery."
Napolitano defended the director of national intelligence, James Clapper, who didn't know about a roundup of terrorist suspects in Britain when asked about the arrests on ABC News earlier this week. The gaffe created an awkward moment for the man in charge of the nation's intelligence community.
Napolitano and President Barack Obama's homeland security adviser, John Brennan, appeared on the ABC show with Clapper. They said Clapper had been preoccupied with handling problems on the Korean peninsula and passage of a nuclear weapons treaty with Russia.
Napolitano said in the CNN interview that homeland security officials were fully aware what was happening in Britain.
"Well, let's be fair," she said. "I knew. John Brennan knew ... So one of the things I think that should be very clear to the American people is that those of us in homeland security who needed to know, we knew."
Officials have said that Clapper hadn't been briefed on the headline-making arrests before being interviewed on ABC News.