"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.
-AAP