Air traffic controllers say the damage to the control center outside Chicago is unlike anything they have seen before.
Critical communications equipment to manage planes in the skies will have to be replaced. The FAA said Sunday evening that it would take until Oct. 13 - more than two weeks - to get the facility up and running at full capacity.
Until then, there will continue to be significant disruptions to air travel in the region.
The damage at the control center in suburban Aurora resulted from a fire allegedly set by contract worker Brian Howard, who was found in the facility's basement with self-inflicted knife wounds. He is recovering from those injuries and faces a felony charge in the case.
Sunday marked the third day of delays and cancellations as airlines advise passengers to adjust their plans. More than 700 flights were canceled.
"It's been about two days since I was supposed to take off," one passenger said.
Some airlines are reporting progress. Delta says it didn't cancel any flights into or out of Chicago today related to the fire.
The FAA says it has been able to steadily increase air traffic and reduce delays. The agency's approach has been to shift air traffic management to other regional radar facilities. Now those facilities have had to call in additional help to manage planes taking off and landing in Chicago.
Aviation analyst Josh Marks said the system is less than efficient.
"The FAA air traffic control center is still based on the technology from the 1950s. It has relatively limited flexibility," Marks said.
The system is being put to the test this weekend and the days ahead will bring more challenges.
But one expert says this may still be the best backup plan to have.
"I think the rarity of these instances suggest that if you have a duplicate system everywhere, the cost would be astronomical and just unacceptable," Ken Button, of George Mason University. "But these things do happen on a minor scale - but this is unique as far as I know."