Virgin Blue suffered an outage of its check-in systems on Tuesday afternoon, causing backlogs at airports nationally.
The company issued a statement that pegged the IT glitch at "just a few minutes" in length and played down its impact on passengers.
However, passengers contradicted this version of events on Twitter.
"At 4.46pm the Virgin Blue check-in system had terminal failure. By 5.15pm, the laws of chaos have been put into effect," dain_ger wrote.
"Virgin Blue problems far from fixed. Plenty of delays tonight in Brisbane," another user, emef, tweeted.
"Just landed back in Sydney after farcical virgin blue check-in meltdown in melb. 2 hour delay," larrymcgrath tweeted.
An airline spokesman later told The Sydney Morning Herald there were "going to be delays" as a result of the system outage.
Check-in staff had been forced to revert to manual processes during the outage.
"Our team is doing the best they can to get u flying away asap," Virgin Blue said on its official twitter feed.
"We are experiencing delays as a flow on effect from earlier issues".
Virgin Blue suffered a major outage of its check-in systems in September last year, forcing the cancellation of at least 116 flights and leaving thousands of passengers stranded.
The airline pinned the blame for that incident on its IT outsourcer Navitaire.
A couple of weeks later, it appeared to suffer a fresh round of outages.