A U.S. Department of Homeland Security computer system that checks airline passengers against terrorism watch lists experienced a brief service disruption -- about 90 minutes -- Wednesday night, U.S. Customs and Border Protection officials said.

The problem led to long delays at security screenings at New York City's John F. Kennedy Airport, as well as other entry ports into the U.S., including Boston, Dallas-Fort Worth and Baltimore.

Many passengers took to social media to complain about the delays.

The agency said Customs agents processed international travelers using "alternative procedures" until the systems were back online.

Customs said, "At this time, there is no indication the service disruption was malicious in nature."

Material for this report came from AP and Reuters.