Homeland Security Secretary Janet Napolitano warned Monday that her agency would be forced to furlough 5,000 border control agents under mandatory spending cuts, likely allowing more illegal immigrants into the country and potentially compromising national security.Napolitano said the cuts, known as the sequester, would disrupt the Department of Homeland Security’s ability to conduct customs inspections at ports, leading to increased waiting times for travelers and cargo shipments. Disaster relief funding would be reduced by $1 billion, she added, meaning relief for victims of natural disasters like Hurricane Sandy and tornados in Joplin, Mo., and Tuscaloosa, Ala., could be cut.

At the borders, Napolitano said the department would have to scale back patrols between ports of entry in the southwest United States, after years of making progress in stopping people from entering the country illegally from Mexico.

Asked if the cuts would make the country more susceptible to acts of terrorism, Napolitano said: “It’s always a threat. We do what we can to minimize the risk, but the sequester makes it awfully, awfully tough."

Napolitano was the latest Obama administration official to sound public alarms over the mandatory spending cuts, which are set to kick in Friday unless the White House and Congress agree on a plan to divert or delay them. Administration officials have warned of cuts to emergency responders such as police and firefighters, massive furloughs of civilian staff at the Pentagon and delays of up to 90 minutes at airports during peak travel hours.

The U.S. Customs and Border Protection department faces $754 million in cuts, the agency said last week, and it would be forced to cut overtime pay, which is critical to staffing border patrols. That department plans to furlough agents up to 14 days this year.

Napolitano, who detailed the plan in the White House briefing room, noted that the cuts to border control come during a political debate over comprehensive immigration reform. Republicans have called on the White House to devote more resources to border control, even as administration officials cite beefed up enforcement operations in recent years.

Some GOP leaders in Congress have said they will not support offering the estimated 11 million illegal immigrants a path to citizenship until the border is more secure.

“Reducing the number of border control agents does affect our ability to keep out illegal immigrants out of the country,” she said.