Almost 100 domestic Jetstar flights will be cancelled this weekend when the airline's pilots are expected to walk off the job demanding a pay rise.

Key points: Jetstar pilots will walk off the job on Saturday and Sunday for four hours demanding better pay and working conditions

Jetstar pilots will walk off the job on Saturday and Sunday for four hours demanding better pay and working conditions The airline will cancel 44 services on Saturday and 46 on Sunday

The airline will cancel 44 services on Saturday and 46 on Sunday The pilots' union said industrial action would not be taken over the Christmas and New Year period

Jetstar chief executive Gareth Evans said Qantas would schedule extra flights while Jetstar consolidated services by moving passengers onto other flights.

About 80 per cent of flights were expected to operate as scheduled.

"We're cancelling approximately 44 and 46 flights on Saturday and Sunday with a view to getting over 95 per cent of our customers away on their original day of travel," Mr Evans said.

Passengers with flights booked between December 13 and 20 could also receive a full refund.

The impact on Jetstar's international flights was expected to be minimal.

It comes after the airline was challenged with lengthy delays and cancellations on Tuesday because of an IT outage that affected its check-in counters at airports around the country.

The Australian Federation of Air Pilots (AFAP) and Jetstar are in dispute over pay and working conditions.

Mr Evans said the strike was "unjustified".

Pilots will walk off the job for four hours this Saturday and Sunday. ( ABC News: Xavier La Canna, file photo )

"We're committed to reach an agreement that rewards our people for the great work that they do every day but not at any cost," he said.

"The union is demanding a 15 per cent wage rise in the first year of the agreement and to do that would put unsustainable upward pressure on the low fares that have been the core of Jetstar since inception."

But in a statement, AFAP executive director Simon Lutton said that was incorrect.

"Assertions by Jetstar that we are seeking a 15 per cent wage increase are simply untrue. The AFAP wage claim is for 3 per cent annual increases to salary," he said.

Mr Lutton said Jetstar had "manufactured" the 15 per cent increase based on "flawed costings of our non-salary claims".

He said the decision to strike had "not been made lightly" and that industrial action would not take place between December 21 and January 3.

About 18 additional flights will also be cancelled on Friday across Sydney, Melbourne, Avalon, Brisbane, Cairns and Adelaide airports when 250 Jetstar baggage handlers and ground crew walk off the job for two hours demanding guaranteed hours of work and a wage increase.