While saying that she was always looking to improve the security systems in place, Ms Napolitano added that the new technology and the pat-downs were "objectively safer for our travelling public".
She dismissed a recent news report about major airports failing secret tests designed to get contraband such as guns and knives past security screeners. The report said some airports had a 70 per cent 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"Many of them are very old and out of date and there were all kinds of methodology issues with them.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. "We pick up more contraband with the new procedures and the new machinery."
Ms Napolitano defended the director of national intelligence, James Clapper, who did not know about a round-up of terrorist suspects in Britain when asked about the arrests television earlier this week, an awkward moment for the man in charge of the US's intelligence community.
Ms Napolitano and President Barack Obama's homeland security adviser, John Brennan, appeared on television with Mr Clapper. They said Mr Clapper had been preoccupied with handling problems on the Korean peninsula and the passing of a nuclear weapons treaty with Russia.
Ms Napolitano said in the CNN interview that homeland security officials were fully aware of what was happening in Britain.
Officials have said Mr Clapper had not been briefed on the headline-making arrests before being interviewed on ABC News.
Mr Obama condemned what he said was an "outrageous" terrorist attack in Pakistan that killed at least 45 people.
A female suicide bomber threw hand grenades, then detonated an explosive belt at an aid distribution centre.
It is believed to be the first time Islamic militants have sent a woman to carry out a suicide attack in Pakistan.