The agency must cut about $754 million from its budget by Sept. 30 as part of the automatic government spending cuts known as the sequester.
David Aguilar, the agency's deputy commissioner, said it will make the cuts with agency-wide furloughs, a hiring freeze and reducing or eliminating overtime, compensatory time, travel and training, CNN reported.
Employees were notified Thursday of the changes.
The furloughs will begin in mid-April, the agency said.
The agency "continues to evaluate further impacts of sequestration" on its operations, Customs spokeswoman Jenny Burke said.
"Even with these cuts, though, individuals apprehended illegally crossing the southwest border will still be processed as usual," she said.
Other agencies are making similar cuts to reduce their budgets.
Homeland Security Secretary Janet Napolitano said early in the week she expects customs "wait times" to increase by 150 to 200 percent.
"I don't mean to scare, I mean to inform. If you're traveling, get to the airport earlier than you otherwise would. There's only so much we can do with personnel," Napolitano said.
The National Treasury Employees Union, which represents about 24,000 Customs and Border Protection workers, says the staff reductions will undercut national security.
"There is no escaping the reality that sequestration is having serious effects on the traveling public and on vital commerce," said Colleen M. Kelley, the union's president.