Pacific Blue says domestic airline passengers are facing short delays after its computer system failed for the second time in four days.
The airline says staff had to revert to manual check-ins for a short time on Wednesday morning but the system is now up and running again.
However, Virgin Blue, the parent airline, is experiencing problems with its computer system at Brisbane airport.
The airline's hardware system crashed on Sunday, causing flight delays and cancellations for two days.
The ABC reports the airline has blamed Navitaire, its information technology contractor, for the disruption and legal action is being considered.