At her first hearing before the House Homeland Security Committee, Napolitano said the 2012 deadline set by Congress is not going to work.
"To do 100 percent screening requires agreements with many countries," Napolitano said, echoing a position taken by officials in the Bush administration.
A law passed by Congress in 2007 requires the Homeland Security Department to screen all cargo headed for the United States by 2012. About 11.5 million containers come into the U.S. each year.
Total screening also could significantly slow commerce at busy ports, and at least 27 countries and major industry associations have raised significant concerns with how they would be affected by the law.
Among the major obstacles to meeting the deadline is deploying trained U.S. officials to more than 700 foreign ports to operate scanning equipment.
Napolitano said the agency currently screens almost all cargo containers considered suspicious. She has said she agrees with the concept of catching threats before they reach the United States.
Napolitano also was chided at the hearing for not talking "terror."
Before the former Arizona governor began her testimony, Rep. Peter King, the panel's ranking Republican, noted to Napolitano that "the word 'terrorism' isn't used" in her prepared remarks. "I think it's important for people like us in positions of leadership to constantly remind people" about the threat of terrorism, the New York Republican said.
Napolitano's prepared testimony, obtained in advance by CBS News, did not include the word "terrorism," but the secretary inserted it in response to Rep. King's observation. As she described the Department of Homeland Security's mission to be protecting the nation from threats "both natural and manmade", Napolitano added, "And terrorism, Mr. King, I believe falls into that category and is central to the category."
Unlike her predecessors, Napolitano used less terror-specific rhetoric when discussing the agency. At one point she said the issue for the department when dealing with terrorism is "How do we respond and recover with resiliency and efficiency."
Not all of her congressional questioners objected to the apparent shift in focus. "I applaud the new tone of the department," said Rep. Jane Harman, chairman of the Subcommittee on Intelligence, Information Sharing and Terrorism Risk Assessment, adding that the role of the department "is to prepare, not scare."
From day one, Napolitano has avoided the nearly constant terror-talk of her two predecessors at the department, created in the wake of the 9/11 attacks, reports CBS News' Carter Yang.
At her first meeting with beat reporters at Homeland Security headquarters on January 30, nine days after she was sworn-in, the new secretary's tendency to nix the word "terrorism" was evident as she spoke for more 30 minutes about the northern and southern borders, immigration, the ice storms in the Midwest, hurricane preparations, and other issues without explicitly mentioning terrorism.
In a one-on-one interview following the session, CBS Correspondent Bob Orr pressed the incoming secretary on the subject, asking her if terrorism would remain the top priority at DHS under her tenure. "It's a top priority," Napolitano answered.
In her testimony, Napolitano mentioned "technology," "border" and "protect" most often and talked about holding department employees accountable and spending taxpayer money wisely, although she made clear that the department's responsibility is protecting the nation against terrorism.
She is the first secretary to use a Capitol Hill debut to talk about hurricanes and disasters, a sign of the department's evolving mission following Hurricane Katrina.