Jetstar is preparing to make major flight schedule changes through January in anticipation of pilot strikes continuing into the new year, as it braces for pilots to walk off the job this weekend.

The brewing industrial dispute comes as the Qantas-owned budget carrier was hit by lengthy delays and cancellations on Tuesday due to an IT outage that affected its check-in counters at multiple airports across the country.

Jetstar's pilots and ground crew are preparing to walk off the job this weekend. Credit:Rob Homer

On top of the dispute with pilots, 250 Jetstar baggage handlers and ground crew will hold two two-hour stop-work meetings at various times on Friday at Sydney, Melbourne, Avalon, Brisbane, Cairns and Adelaide airports.

Australian Federation of Air Pilots members, who make up around 80 per cent of Jetstar's mainline pilots, will walk off the job for four hours on Saturday and Sunday amid stalled wage negotiations.