Air Canada is expecting a return to full service on Saturday after winning a government order to end an “illegal” work stoppage by its pilots.

Earlier Friday the airline issued a nationwide travel alert warning of cancellations and delays across the country after some of its pilots called in sick, resulting in around 75 cancelled flights at Pearson International Airport.

The affected flights were mostly to and from Toronto.

The company is waiving fees for customers who had to change flights.

In a release Friday, the airline said the Canada Industrial Relations Board granted an order declaring the job action illegal. The board also ordered the pilots union (ACPA) to take all reasonable steps to “bring to an end the illegal strike.”

“Our first priority today has been to take care of our customers,” said Duncan Dee, Air Canada’s Executive Vice President and Chief Operating Officer.

“While we were able to re-accommodate almost all customers affected on alternate flights, we recognize the inconvenience this job action has caused to our customers.   We thank them for their patience and loyalty as we re-double our efforts to restore their confidence in Air Canada.”

Air Canada maintains the job action was undertaken by a small percentage of employees.

“The vast majority of Air Canada’s pilots reported to work today and performed their duties as the true professionals they are.  I would like to thank them and all other Air Canada employees for getting our customers to their destination safely and as quickly as possible,” Dee said.

Passengers were also disrupted in Montreal, Ottawa, Vancouver, Calgary, Edmonton and Winnipeg.

A source told CityNews that a group of pilots planned to book off sick on Friday in Toronto, Montreal and Vancouver to protest recently implemented back-to-work legislation that forced the pilots into binding arbitration.

“We just want to talk with the airline and work out a fair deal,” the source said.

Friday’s action – which followed a similar action last month that saw pilots call in sick and flights cancelled across Canada – was unsanctioned by the Air Canada Pilots’ Association (ACPA).

“We have no way of verifying these allegations [of pilots calling in sick when fit to fly]. We do know, however, that if the allegations are accurate, they have not been initiated or sanctioned by ACPA,” Captain Jean-Marc Bélanger, chair of the union’s master executive council, said in a statement Friday.

“ACPA has not and will not condone using the Canadian Aviation Regulations (CARS), which spell out the rights and obligations governing pilots who are not fit to fly, for industrial action.”

Pearson officials are reminding travellers to check their flight status before heading out to the airport. For the latest updates, click here.

Labour relations at the airline have worsened since the federal government passed back-to-work legislation on March 14 for about 3,000 Air Canada pilots and about 8,600 ground workers, including baggage handlers and mechanics. Negotiations between the workers’ unions and the airline have been forced into arbitration.

Air Canada pilots claim the government’s intervention violates their Charter rights and their union filed a constitutional challenge in Ontario court.

On March 22, the airline’s ground crews staged a wildcat strike after three workers were suspended for allegedly heckling federal labour minister Lisa Raitt. Air Canada issued a cease-and-desist order about 12 hours after the illegal labour action began.