While Customs said its systems were restored by about 10 p.m., airports warned passengers to expect delays tonight.
US Customs and Border Protection said on its Twitter page that there was "no indication the disruption was malicious in nature". It gave no explanation for the disruption and said travelers were processed using alternative procedures.
"During the technology disruption, CBP had access to national security-related databases and all travelers were screened according to security standards", the agency said in a statement.
CBP officers continued to process worldwide passengers using alternative procedures, but the agency acknowledged that travelers at some ports of entry experienced longer than usual wait times.
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JFK International, Dallas Fort Worth International as also some others acknowledged the delays on Twitter.
The people entering the United States have posted their images on different social media sites of long lines at Hartsfield-Jackson Atlanta International Airport and John F. Kennedy International Airport. Seems like their system did completely go down.
It's a rough night for global travelers at Miami worldwide Airport. A similar outage had hit computer systems a year ago.
A computer fault at several major U.S. airports left hundreds of holidaymakers queuing for "about two hours" to enter the country on Monday evening.