Passengers of Jetstar, Virgin Australia and Tiger Airways suffered on Saturday from chaos as the check-in system in Melbourne, Brisbane, Perth and Sydney Airport crashed for two hours due to a computer glitch.

Plane departures were delayed and long lines of travelers were seen in the four airports as staff manually checked in passengers one at a time. In Sydney, the lines were up to over 50 metres long and snaked outside the drop-off zone.

Although by midday the IT outage was fixed, the three airlines struggled to address the backlog caused by the glitch.

To appease angry passengers over the delays, Jet and Virgin gave bottled water to flyers and $8 food and drinks vouchers that could be redeemed at the terminals.

"The system is back up and running now, but we are still expecting delays. It's a domino effect as the same plane makes flights out of multiple airports throughout the day. Sydney, Melbourne, Brisbane and Perth are taking the brunt," News.com.au quoted Virgin Australia spokeswoman Melissa Thomson.

Because of the Navitaire system computer crash, the improvised passenger boarding passes issued at Sydney Airport resulted in no seat assignments. Travelers were allowed to sit anywhere they like according to their class.

The delays at Tullamarine Airport in Melbourne for Jetstar and Virgin Australia trips lasted up to four hours. Passengers decried the confusion and lack of communication from the affected airlines.

It was not the first Navitaire system crash. A similar incident happened in 2010 which resulted in two days of flight cancellations and delays for Virgin Blue passengers. The air carrier considered filing a lawsuit against Navitaire but reached a confidential settlement in 2011.

Due to these incidents, Virgin will migrate to a new IT system in 2013 and ditch

Navitaire, Ms Thomson said.

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