"I would say 150 to 200 percent, as long as what we would normally expect," Napolitano said. "We will see these effects cascade over next week."
Officials say it's due to cuts in overtime. With furlough notices set to go out this week, it will likely only get worse.
The excruciating wait times are not just felt by travelers entering the U.S. going through customs.
In a statement, the Transportation Security Administration said, "due to the reductions mandated by sequestration, TSA will put in place a hiring freeze which will result in up to an additional 1,000 TSO vacancies by Memorial Day weekend and up to 2,600 vacancies by the end of the fiscal year."
For travelers, fewer security screeners means more time in line. The TSA said wait times could double to more than an hour during busy travel periods.
The Associated Press contributed to this report.