Air traffic returned to normal after a problem believed to be a software glitch was fixed, the Federal Aviation Administration said.

The FAA grounded hundreds of planes Tuesday after an apparent breakdown in the program the agency uses to log flight plans, but the matter was resolved by late evening.

"Everything's back to normal," FAA spokeswoman Diane Spitaliere told FOXNews.com Wednesday. "[The problem] was cleared up late last night."

At least 646 flights were affected Tuesday following a communications failure at an FAA facility in Hampton, Ga., that had an impact on airports across the country.

Most flights were delayed by 90 minutes. Atlanta, Chicago and Charlotte airports were the hardest hit and other hubs in the Northeast also were affected, according to the FAA.

The FAA said travelers should still check the status of their flights Wednesday morning.

Officials speculated that a software failure led to the communications breakdown.

At 1:30 p.m. Tuesday, the National Airspace Data Interchange Network in Hampton crashed, and its flight plans had to be routed to a similar NADIN facility in Salt Lake City, which then became overloaded.

FAA employees in Atlanta entered some of the flight plans by hand to keep the Salt Lake City network from crashing. The two facilities process all flight plans for commercial airliners in the U.S.

Thousands of travelers were stranded as the FAA struggled to manage the flight information, which had to be filed before the planes could leave.

"Planes must file a flight plan to take off," said FAA senior spokeswoman Laura Brown. "Without that, they sit on the ground."

The NADIN system was restored at 7 p.m. Tuesday and was fully functional by 1:15 a.m., according to spokeswoman Kathleen Bergen. The FAA put the system back online gradually to prevent another shutdown during evening rush hours.

FAA officials said they were not sure what caused the initial failure but were collecting information to determine how to prevent such a glitch in the future. They said a similar problem occurred June 21 on a much smaller scale.

"We're still trying to find root causes of the problem," said Spitaliere.

FAA officials said they are in the process of replacing the NADIN computer systems in Salt Lake City, but that overhaul was not the cause of Tuesday's crash.

The Department of Homeland Security confirmed that the delays were not terror-related.

"Hacking does not appear to be an area (of concern)," said Hank Krakowski, chief operations officer for the FAA. "Right now it looks like an internal software processing failure in the area. We actually think we know what it is; we're in the process of determining what it was right now."

Bergen said safety was never an issue during the breakdown, and that officials were still able to speak to pilots in planes on the ground and in the air.