The computer at WestJet's Calgary headquarters that generates flight plans stopped working properly for two hours late Sunday afternoon.
Airline spokesman Robert Palmer says that meant WestJet (TSX:WJA) staff had to generate the flight plans manually, which took longer.
"The system was back up and running last night and today we are operating normally," Palmer said in an email. "Our IT team is working to determine the cause of the problem yesterday."
A total of 12 flights were cancelled Sunday and Monday affecting Toronto, Hamilton, Ottawa, Montreal, Halifax, Calgary and Vancouver. Ten of those were out of Toronto's Pearson International Airport.
Palmer said WestJet expects no further cancellations.
About 95 flights were delayed, mostly on Sunday, as a result of the glitch.