"Customs and Border Protection has nationwide outage. Expect delays in passenger processing until the system is restored," Fort Lauderdale's airport, a major hub for the United States and Caribbean, said on Twitter.
A Customs and Border Protection department spokesman told NBC News that there had been a disruption at several airports and was "taking immediate action to address the technology disruption."
But that was not immediate enough for the thousands of tired and cranky passengers arriving at US gates but unable to clear customs.
Miami International tweeted its regrets for the delays.
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"They are working to restore," it said on Twitter.
But there seemed to be little information and guidance for the thousands stuck in travel limbo.
"People are starting to argue and get frustrated," Cali Rez tweeted in Miami. "Get someone down here to explain things and direct the lines ASAP."
The airports are known to include Miami International, Atlanta Hartsfield, Boston Logan and Fort Lauderdale, officials said.