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.

Travellers were delayed at airports nationwide after the Navitaire check-in system failed.

The outage meant airlines including Jetstar, Virgin, Tiger and Rex had to check passengers in manually, causing several flights to be delayed.

Tiger Airways spokeswoman Vanessa Regan said the Navitaire system came back online this afternoon.

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,'' 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.

LONG QUEUES

Sydney Airport was left in chas after the system outage.

Jo Ramsbotham, a former flight attendant, stood in the same spot in the JetStar check-in queue for half an hour.

She arrived at 10am and heard announcements about a terminal outage minutes later.

"I fly often and haven't experienced this before. If I was elderly I would have had a nervous breakdown, [we've] been waiting so long," she said.

People complained about a lack of announcements, saying the speaker volumes are too low.

Greg Argent and his partner Megan Norman planned their week-long Gold Coast holiday with another family, towing along five children from ages seven to 12.

Their flight JQ408 was supposed to depart at 11am but 40 minutes later they were still waiting to be manually checked in.

"It's a schmozzle, this is terrible," said Argent. "We had plans to go to theme parks this afternoon but now that's all cancelled. This kids are disappointed."

"We got here one and a half hours before our flight. We had to go find someone with an orange uniform to get information," said Norman. "We can't hear the announcements because it's so loud."

- AAP