The problem lasted about 90 minutes and there have been no indications the technology disruption was malicious in nature, US Customs and Border Protection said in a statement.
During the outage, Customs and Border Protection officers processed international travelers using alternative procedures, the agency said.
Customs and Border Protection did not specify which US airports experienced disruptions, but NBC News reported delays in security screenings at New York City's John F. Kennedy Airport.
Similar problems were reported in Boston, Dallas-Fort Worth, Charlotte, North Carolina, and Baltimore, it said.
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