LAX, John Wayne Airport in Orange County, Ontario International Airport and Bob Hope Airport in Burbank were among the airports affected by the order that prevented flights from departing.
Some airports used their official Twitter accounts to say their flights were departing, including McCarran International Airport in Las Vegas, Bob Hope Airport and San Diego International Airport.
The computer problems occurred at the Los Angeles air traffic control center, FAA spokesman Ian Gregor said.
Incoming flights were reportedly diverted to other airports not affected by the glitch, disrupting travel plans.
The agency issued a nationwide ground stop for those heading into the airspace managed by the center.
Airport officials urged passengers to check with their individual airlines for flight information.
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