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The second such problem to hit the network in just over a year began at 5am but was repaired within four hours, the Federal Aviation Administration (FAA) said.
"A router problem disrupted a number of air traffic management services, including flight plan processing," it said in a statement, blaming the failure on software malfunction at an FAA site in Salt Lake City, Utah.
The Atlanta-based National Airspace Data Interchange Network, which processes flight planning, was also affected as it relies on data from the FAA Telecommunications Infrastructure in Salt Lake City.
"As a result, FAA services used primarily for traffic flow and flight planning were unavailable electronically," the agency said.
An investigation has been launched, but the FAA ruled out a cyber attack.
"During the outage, air traffic controllers managed flight plan data manually and safely according to FAA contingency plans," the FAA statement added.
An FAA spokesperson, Diane Spitalieri, told AFP the problem was "system-wide" and had been "slowing down the system significantly."
Hartsfield-Jackson Atlanta International Airport, Atlanta, one of the world's busiest serving over 90 million passengers each year, was one of the worst affected hubs.
Dozens of flights cancelled
But passengers and airlines across the East Coast also experienced travel chaos even after the system was up and running again.
"There are some residual delays because of this, but I am not sure of the number," said FAA spokeswoman Tammy Jones.
By early Thursday, AirTran Airways, which operates out of Atlanta, had been forced to cancel 38 flights around the country, spokesperson Christopher White told AFP.
"The ripple effect — regardless of when this system gets back online — will be felt throughout the day," he said, urging passengers to check the status of their flights online first before heading to the airport.
The problems were further compounded by poor weather conditions in much of the northeastern United States.
"Due to lingering effects from the FAA computer issue earlier today, airlines at both O'Hare and Midway International Airports are still reporting flight delays," the Chicago Department of Aviation said in a statement.
Delays were reported of between 20 to 30 minutes at the two airports, with a few cancellations. Flights to and from the East Coast were held up for 90 minutes.
At Newark International Airport outside New York City, the FAA noted that traffic was experiencing delays of at least one hour and 30 minutes.
Washington area airports were posting delays of up to one hour and 15 minutes.
A National Airspace Data Interchange Network malfunction in August 2008 delayed hundreds of flights in the eastern part of the country, causing the FAA to shift processing to its backup location in Salt Lake City.
AFP
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