UPDATE 11:24am: Flights at Australian airports are expected to begin running as normal after a three-hour failure of the check-in system used by Jetstar, Virgin and Tiger Airways was fixed.
There are chaotic scenes at several departure terminals with Perth, Brisbane, Sydney, Adelaide and Melbourne all reportedly affected by the technical glitch.
It is believed that the Virgin system shut down nationally before around 7.30am AWST this morning.
Three flights checking-in at Perth Airport were affected, with all check-ins now being done manually until the systems picks back up.
Tiger Airways spokeswoman Vanessa Regan said the Navitaire system came back online just before 10am (AWDT) on Saturday.
She said the outage had caused a half an hour delay for several Tiger flights.
"We did have a couple of minimal delays but we expect to smooth those over now," Ms Regan said.
Virgin Australia spokeswoman Melissa Thomson said check-in processes had returned to normal and the airline would work to minimise delays.
A Jetstar spokesman said the outage caused delays across the airline's network and staff were working to process delayed passengers as quickly as possible.
"We know that this has inconvenienced our customers and we thank them for their patience as we process passengers," he said.
A Navitaire system crash in 2010 caused chaos for Virgin Blue passengers nationwide, with two days of flight cancellations and delays, forcing some to put themselves up in hotels.
Virgin boss Richard Branson apologised, saying it had been a "terrible 24 hours".
The airline blamed Navitaire for the chaos and said it was considering legal action, but reached a confidential settlement in 2011.
Ms Thomson said Virgin was migrating to a new IT system next year and would no longer be using Navitaire.