Arizona Governor Napolitano Emerges as Obama's Top DHS Pick

Aside from immediate concerns about attacks, DHS will also be dealing with immigration and border security.

As the governor of a border state, Napolitano touts her actions as the first governor to ask for the National Guard to be posted at the U.S-Mexico border. She also called for federal funding to cover the move.

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While the issue was barely discussed during the presidential campaign, the Obama camp has taken a position that, according to the campaign's Web site, supports "a system that requires undocumented immigrants who are in good standing to pay a fine, learn English, and go to the back of the line for the opportunity to become citizens."

Aside from immigration as a leading policy issue, the next secretary will also have to deal with information-sharing as a continuing challenge, as the agency continues to evolve and build a more robust response to natural disasters such as hurricanes.

During his campaign, Obama noted that securing nuclear weapons and bio-security issues topped his domestic security agenda. Both issues will be a challenge for the agency, as a recent report by the Government Accountability Office found that the effectiveness of nuclear-detection systems has been exaggerated by DHS officials working on the issue.

With economic uncertainty ahead, funding of such expensive systems could be an issue. "The response to threats has been to throw money at the problem and look for a technological advantage. ... I don't think they will have the type of money that they have," Rojansky said.

The effectiveness of bio-security programs also remains unclear. DHS is designing new detection system under its bio-watch program. Its bio-surveillance system was compromised in 2007 when a man infected with a virulent form of tuberculosis gained entry into the United States, despite his being on a watch list.