The check-in system crashed just after 8 a.m., sending travel plans into chaos with some flights cancelled, Sydney Morning Herald reported.
"We've been advised the cause is an external supplier's hardware failure," Colin Lippiatt, manager of corporate communications for the Virgin Blue group of airlines, said.
He said measures had been taken to rectify the problem but the automated system had to be tested before it could be started up again.
The computer problem affected Virgin Blue flights at airports across the country, as well as the web check-in service, and some Virgin Pacific international flights, Lippiatt said.
As a result, airport staff switched to manual check-in and boarding procedures.
"Obviously it's causing long delays and some cancellations through the morning and day," Lippiatt said.
He could not confirm the number of cancelled flights but agreed there was "distinct possibility" delays would be experienced for the rest of the day.
Published 26 September 2010, 05:23 IST