Updated 09/26/14 – 2:31 p.m.

CHICAGO (CBS) — Several hours after an apparently disgruntled contract worker set a fire at a Federal Aviation Administration radar center in Aurora, the facility was still considered a crime scene Friday afternoon, and limited flights were operating at O’Hare and Midway airports.

The damage to the Chicago Air Route Traffic Control Center in Aurora created a ripple effect across the nation’s air traffic system, forcing many flights to be cancelled or delayed outside the Chicago region.

Some flights in and out of O’Hare and Midway airports resumed operations “at a reduced rate” late Friday morning, but only a small fraction of the airports’ normal flight load.

Aurora Police Chief Greg Thomas said investigators believe a 36-year-old contract employee for the FAA lit several fires inside the basement telecommunications room of the FAA Chicago Air Route Traffic Control Center in Aurora. He suffered burns on his body, and self-inflicted stab wounds on his arms. He was being treated at an Aurora hospital.

The FBI, FAA, ATF, and Aurora police and fire officials were conducting a joint investigation. The FBI later announced that Brian Howard of Naperville had been charged in connection with the fire and air-traffic disruption.

By Friday evening, airlines had canceled nearly 1,550 flights today at O’Hare. Flights that were still scheduled were being delayed by as much as three hours, the city’s Aviation Department said.

At Midway, airlines canceled more than 470 flights. Southwest Airlines has suspended all flights for the day.

ATF spokesman Tom Ahern said the man, a Naperville resident, was authorized to be in the telecommunications room, but Ahern did not know what the employee’s job responsibilities were. No guns or explosives were found at the scene, according to Thomas. Authorities also could be seen removing a dark blue or black SUV from the facility late Friday morning.

“We don’t know what his motive was at this point,” Ahern said.

A second employee, a 50-year-old man, suffered smoke inhalation from the fire, and was treated at the scene.

Thomas said there was no evidence of a terrorist act, and it appeared to be an isolated incident.

“There is no reason to believe anyone else was involved at this time,” he said.

CBS 2’s Jay Levine reports the damage to the computers that control the facility’s radar and communications systems is extensive, and could keep the building out of commission for days.

Thomas said police and fire crews responded to a fire at the facility at about 5:45 a.m. The fire was quickly extinguished, but the fire forced officials to evacuate the radar facility.

Authorities said the telecommunications room was still a crime scene Friday afternoon, as investigators processed evidence.

“There’s a great deal of work that still has to be done,” Ahern said.

Authorities said they could not confirm or deny news reports that the employee wrapped gasoline-soaked rags around transmission lines in the basement.

As of 2:15 p.m., nearly 1,400 flights had been canceled at O’Hare International Airport as a result of the fire, and nearly 400 were canceled at Midway International Airport, according to the Chicago Department of Aviation.

The ground stop created a nightmarish ripple effect for travelers across the country, with several flights canceled at Milwaukee’s General Mitchell Airport, and many flights at other airports across the country delayed or rerouted because of the fire at the Aurora radar center.

Southwest Airlines, the largest carrier at Midway, has canceled all of its flights for the day. AirTran, which is undergoing a merger with Southwest, was assessing whether it could get any flights out amid the reduced operations.

Airports in Wisconsin and Iowa also were being impacted by the fire at the radar facility. FAA spokeswoman Elizabeth Isham Cory said airspace management duties at the Auror radar center have been transferred to other air traffic facilities.

The facility in Aurora is home to some of the most sophisticated radar equipment in the nation, and is used to track flights that travel across parts of five states – Illinois, Indiana, Iowa, Michigan, and Wisconsin. Controllers at the facility handle millions of flight operations a year, tracking flights, adjusting speed and altitude for planes, and keeping them at safe distances.

The National Air Traffic Controllers Association said the FAA’s Indianapolis Center was bearing the brunt of the extra workload from the evacuation of the Aurora radar facility.

“They are doing what they can to support. They have one route for Chicago-area arrivals currently in operation, and are considering ways to add a second. They’ve also developed a non-radar departure route for southbound departures out of the Chicago area. Additionally, they are preparing to handle an increased load of East Coast traffic. In short, they’re doing everything they can to assist,” NATCA officials said in an email.

With no flights going in or out of either Chicago airport Friday morning, the skies above northern Illinois, southern Wisconsin, and parts of Iowa, Indiana and Michigan were virtually empty, as seen in the radar image below from FlightAware.

This is the second time in four months that an emergency at an FAA radar facility has forced airlines to halt flights at Midway and O’Hare. In May, smoke at the TRACON facility in Elgin halted flights at the two airports for more than three hours. More than 1,000 flights were canceled at O’Hare, and another 120 were canceled at Midway. More than 1,400 other flights were delayed.