"If it's continued into next year, that means issues about personnel and it also means then that people will experience longer lines, longer wait times, all those sorts of things," Napolitano told the paper.
The Transportation Security Administration (TSA), which conducts airport security operations, is overseen by the Homeland Security Department.
When the sequester was first implemented, Napolitano warned of the possibility of longer airport security lines. Critics argued she and other Obama administration officials were using scare tactics to win the political argument with Republicans over the budget.
Napolitano told the paper that she was not crying wolf on the way out of the door with her warning about the possibility of longer security lines next year.
"You always hear that line: you need to do more with less," Napolitano said. "But sometimes you're at the point where you can only do less with less."