The union representing Air Canada pilots is challenging allegations that some members called in sick on the weekend to make trouble for the airline.

"Why does Air Canada not take ownership of its problems rather than always blaming someone else?" asked Paul Strachan, president of the Air Canada Pilots Association.

On Saturday, more than 20 flights were cancelled or delayed between Montreal and other cities including Toronto, Halifax, Saint John, N.B., and some American destinations.

That day, a source at Air Canada mentioned a number of pilots had called in sick, but could not say if it was a factor in the cancellations. Officially, the airline would only say it was facing "a number of operational challenges" during what was considered to be a peak travel weekend at the tail end of the March Break.

Strachan said the cancellations had little to do with sick calls and that the airline is trying to undermine the union.

"There was fog all over the place on Saturday," he said, adding that a number of the cancelled flights were Jazz or Sky regional airlines which employ pilots with different unions.

There were more delays and cancellations Sunday due to fog and a fire on an airfield at Toronto's Pearson Airport.

Air Canada has filed a complaint with the Canada Industrial Relations Board, arguing that there has been a marked increase in sick calls and that it's part of a concerted illegal strike action.

The airline and pilots are embroiled in a bitter labour dispute with the main issues being Air Canada's desire to start a low cost airline and concerns over pension security. The government had forced both sides into mediation that had just begun when Air Canada served notice to lockout the pilots at the same time that the airline's machinists union had given notice to strike.

Federal Labour Minister Lisa Raitt referred the matters to the CIRB to determine if there are health and safety reasons to prohibit a work stoppage. The Conservative government went on to pass back-to-work legislation, imposing final offer arbitration.

There have been emails over the past month from the union to the pilots reminding them they are obligated under law to self-assess whether they are fit to fly or not and that increased stress, due to these tense labour relations, might mean they are not.

In response to that correspondence, Air Canada sent a memo to the pilots warning them that it would be monitoring attendance and that it would take action if it sees any concerted effort at creating work slowdowns.

"We fully support pilots' legitimate rights to withdraw from flying and only fly when they feel it is safe to do so," said Air Canada spokesperson Peter Fitzpatrick in an email to CBC. "What we do not support is pilots removing themselves from duty as part of a labour action."

Strachan said the pilots association has until Thursday to respond to the CIRB complaint and then Air Canada has the opportunity to respond before the board decides if there will be a hearing on the matter.

The pilots argue they are simply following the law.

"Priority number 1 is the safety of the pilots and passengers," Strachan said. "There's a lot of stressors going on right now. What we're saying is now is not the time to pretend you're super human."

Meanwhile, the pilots association is filing a charter challenge to the government's back-to-work legislation, Bill C-33.

Air Canada's operations at Toronto's Pearson International Airport appeared to be back to normal early Monday. The airline's online departures schedule showed just a few flight delays.