Air Canada is telling customers they must be checked in 45 minutes before a flight and the policy isn't open to exceptions.

Over the weekend in Whitehorse, passengers who had arrived about an hour before the flight but were still waiting in line at the cut-off time found themselves out of luck.

Passengers said customer service agents told them their computers shut down automatically at the 45-minute deadline and will not accept any further check-ins.

On July 20 in Whitehorse, Chris Hall discovered he wasn't going anywhere with Air Canada when he arrived at the check-in counter five minutes late for the 45-minute deadline to check in.

Air Canada says the cutoff time is built into computers and staff cannot make exceptions. (CBC)

"It's frustrating because the plane is still here for another 40 minutes and I can't get on it and it really doesn't make much sense. Five minutes and now I have to pay $250," he said.

Air Canada declined an interview with CBC but did send an e-mail directing to its website to read the check-in policy.

Hall booked a flight with a competing carrier.

The Air Canada flight was delayed and departed for Vancouver 12 minutes late.