There were 4,491 delays nationwide Monday, according to figures from FlightAware, with the worst of it coming during the evening amid the system outage.
U.S. Customs and Border Protection said the outage lasted from 5 p.m. - 9 p.m. and the agency "took immediate action to address the issue and CBP officers continue to process international travelers using alternative procedures at airports experiencing the disruption," according to an updated statement.
On Twitter, posts showed hundreds of people in line at airports in Miami, Atlanta, New York, Washington D.C. and elsewhere, describing the situation as a "nightmare" and trying to figure out what was happening.
A spokesman for Philadelphia International Airport tells Action News a few international arrivals were affected early Monday evening.
The spokesman said it took a little longer for those passengers to go through customs and immigration due to the CBP issues.
All international flights that would clear through customs have arrived, the spokesman said.
Customs issued a statement saying the agency was experiencing a temporary outage:
"U.S. Customs and Border Protection is experiencing a temporary outage with its processing systems at various air ports of entry and taking immediate action to address the technology disruption," the agency said in a written statement.
"CBP officers continue to process international travelers using alternative procedures until systems are back online. Travelers at some ports of entry are experiencing longer than usual wait times and CBP officers are working to process travelers as quickly as possible while maintaining the highest levels of security."
In Atlanta, CBP public affairs officer Robert Brisley says the outage at the city's airport lasted about an hour from late afternoon into early evening. He said that officers were working to recover quickly afterward but even short outages can lead to backups at the airport, one of the world's busiest.
He said the agency apologizes to travelers who were delayed getting into the country after long flights.
The Associated Press contributed to this report.