At this time, there is no indication the service disruption was malicious in nature. "Thanks for your patience", Miami International Airport said in a Twitter post.
Long lines and delays were report from New York To Denver to Miami.
A spokeswoman for the agency says a two-hour delay starting around 7:30 p.m. EST forced Customs and Border Protection officers to process arriving passengers using backup procedures at some airports.
The outage hit airports at around 5 pm and lasted through 9 pm.
Thousands of passengers reported being stranded at airports across the United States, in a delay that was caused because the passport system across the country was down Monday.
Customs officers still had security to national security databases, Garbis said.
A few minutes later, another tweet said the customs processing issue was resolved.
CBP said travelers at "some ports of entry experienced longer than usual wait times".
All airports are back on line after a temporary outage of #CBP's processing systems.
"The machines for customs and border patrol aren't working, so all the things are printing out with X's on them and everyone's freaking out, so the lines about an hour to get thru", said Brittany Jason.
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.