The report, which states that right wing extremist groups could use the nation's poor economy and the election of the country's first black president as recruiting tools, has come under fire from Republicans who say the Obama administration is unfairly singling out conservatives and military veterans.
But Napolitano said the reports are "not intended to infringe on anyone's constitutional rights by any stretch," during an appearance on CBS' The Early Show Thursday.
"These reports are issued periodically through the intelligence and analysis division of the Department of Homeland Security. And what they are intended to do is to give state, local, tribal law enforcement what we call situational awareness. What's out there? What do they need to be sensitive to?"
The report noted that military veterans who have difficulty reentering civilian life are susceptible to recruitment, as was the case with Timothy McVeigh, whose 1995 attack on a federal building in Oklahoma City killed 168 people. (Click here to read the full report.)
That drew the ire of the House of Representative's top Republican.
"To characterize men and women returning home after defending our country as potential terrorists is offensive and unacceptable," Ohio Rep. John Boehner said.
Napolitano conceded that, if she had it to do over, "perhaps a few words would be changed," but "the overall impact of the report, and the purpose of the report, which was for state and local law enforcement purposes, that remains the same."
Napolitano was speaking from Mexico City, where President Obama is scheduled to meet with Mexican President Felipe Calderon about the drug-related violence plaguing the U.S.-Mexico border.
Calderon has said that guns from the U.S. are a big factor in the problem, particularly since the federal ban on assault weapons expired in 2004. But while the U.S. is taking measures to reduce gun trafficking, Napolitano said the government was not looking to reinstate the ban.
"Well, that simply is not part of the plan that we're talking about here."
Napolitano said U.S. efforts would focus on increasing border checks, utilizing better technology, more manpower and gun-sniffing dogs.
Watch CBS News correspondent Bill Plante's report on President Obama's trip to Mexico and Homeland Security Secretary Janet Napolitano's interview.