Department of Homeland Security Secretary Janet Napolitano had no part in a decision by underlings to release low-risk illegal immigrant detainees as a way to save money before the sequestration and was surprised to learn about it, Napolitano told ABC News in an exclusive interview.
"Detainee populations and how that is managed back and forth is really handled by career officials in the field," Napolitano said.
Napolitano added that the release, which has been criticized by congressional Republicans, was poorly timed.
"Do I wish that this all hadn't been done all of a sudden and so that people weren't surprised by it? Of course," she said.
When asked why the detainees were in jail in the first place, Napolitano replied, "That's a good question. I've asked the same question myself ... so we're looking into it."
Watch Jim Avila's interview with Janet Napolitano Thursday evening on "World News with Diane Sawyer."
With the sequestration deadline looming over the country today, ABC News asked Napolitano if Americans should feel safe waking up in the morning. She said sequestration will have an effect on border security and safety.
"We are always going to put safety first, and that's why we're not going to be abbreviating our safety procedures or any of that," Napolitano said. "But, by way of example, the number of Border Patrol hours that will need to be reduced equates to the equivalent of 5,000 Border Patrol agents."
The cut, she said, would mean "the large narco traffickers, human smugglers," and other bad players could have easier access to the U.S.
"We deal with a lot of bad actors and we will have fewer agents to do that with," she said. "We'll have fewer hours that the Coast Guard is going to be patrolling along our maritime shores."
The secretary stressed that the department will keep safety first but the effects of the sequester are not to be taken lightly.
"Sequestration is a pretty tough nut," she said.
And she insisted, it is not crying wolf to warn citizens they will see longer TSA lines at the airport and longer lines at the border.
"I think a citizen is going to notice. If there's citizens that are trying to go back and forth to Mexico and Canada, to the land ports of entry, where we already have some problems with long lines at very busy times, you're going to see those lines really grow," she said.
This wait increase will also apply to those coming through international airports and needing to go through customs.
"Those lines are going to grow significantly at some of the larger airports," she said. "We're going to have fewer people to do the checks we do. The checks are going to have to be the same. We do those for security reasons. But we're going to, over time, have fewer people to do them."
And while the effects won't be seen the first Saturday following sequestration, the impact could be felt as early as the following week and should be seen as more of an inconvenience than a security concern.
"From this department's standpoint, the longer lines at the ports, the reduction of Border Patrol hours and Coast Guard operations, those are the things that will be most visible," she said.