"Each and every one of the security measures we implement serves an important goal," Napolitano wrote in a commentary published Monday in USA Today.
The enhanced searches went into effect just days after two bomb devices were found in cargo planes bound for the United States several weeks ago. The holiday travel season begins in earnest next week.
"Pat-downs have long been one of the many security measures used by the U.S. and (other) countries," Napolitano wrote, noting the searches are done by an officer of the same gender.
The scanning machines "are safe, efficient and protect passenger privacy," Napolitano said, explaining the images are viewed in a walled-off location.
Unions representing pilots at American Airlines and US Airways last week advised their 14,000 members to avoid the scanners, calling them intrusive and saying they could emit dangerous radiation. A Food and Drug Administration review didn't find any health threat.
"The public is done with their rights being violated," Kate Hanni, executive director of the travel group flyersrights.org, told USA Today. "People are just furious ... ."
Flyersrights leaders said they would ask their 30,000 members to boycott the full-body scanners and insist any pat-down by Transportation Security Administration staff be done in a private room and with a witness present.
TSA Administrator John Pistole called such boycotts "irresponsible" because scanners "may prevent an attack using non-metallic explosives."
Web-based grassroots efforts call on fliers to boycott scanners Nov. 24, the day before Thanksgiving.