Nav Canada spokesman Ron Singer said a flight planning computer crashed resulting in significant delays for flights leaving Pearson, and cancellations and delays for incoming flights.
"To maintain safe operations we are processing flight information manually for departures, and we are now clearing the backlog," Singer said Thursday night in an email.
Singer stressed that the flight planning system problem was not affecting the safe operation of the air traffic control system at the airport.
All radar and surveillance and communications systems are working normally, Singer said.
"Air traffic controllers can see the aircraft and talk to pilots in their airspace," he added.
"The measures we have put in place to manage a safe and orderly flow of traffic, at a slower pace, are intended to ensure safety: unfortunately we regret that this is what has caused delays," he said.
Air Canada told concerned travellers via Twitter that the delays and cancellations were out of its control.
One passenger tweeted that her plane had left the gate "three hours ago" but had not taken off.
"At least waiting for 2 hours in your plane includes free movies, music and plugs. Wanna be home though," another passenger tweeted.