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The Department of Homeland Security computer system that checks airline passengers against terror watch lists briefly experienced service disruptions Wednesday evening that led to some delays, officials said.

Officials told NBC News the system was back up just after 9 p.m. U.S. Customs and Border Protection said the outage lasted about 90 minutes, and that the problem was with processing systems at airports of entry in the U.S.

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"In the meantime, CBP officers processed international travelers using alternative procedures until systems were back on line," Customs and Border Protection said in a statement. "At this time, there is no indication the service disruption was malicious in nature."

The problem caused delays at New York City's John F. Kennedy Airport, NBC New York reported. Federal officials said the problem slowed down screening at several major airports.

Officials said fliers continued to be checked against the terror list during the disruption.

Hartsfield-Jackson Atlanta International Airport in Georgia, Dallas/Fort Worth International Airport in Texas and Charlotte Douglas International in North Carolina were among the airports affected, but airport officials said the impact was minimal.

A passenger at Boston Logan International Airport said computers were down and people were filling out green paper forms.

Electronic kiosks where passengers can fill out self-service declaration forms were down, and there were noticeably more staff at customs counters — "looks like they paged a bunch of people to come in," passenger Jeremy Hitchcock said.

U.S. Customs and Border Protection officials said the problem was with the computers and kiosks used by passengers arriving in the United States at airports nationwide.