A computer problem has disrupted the travel plans of thousands of Virgin Blue passengers who remain stranded at airports around the country.

The airline says the check-in system crashed just after 8:00am AEST.

Virgin Blue spokesman Colin Lippiatt says some domestic and international flights will have to be cancelled and others are facing long delays.

Investigations are underway into what went wrong.

He says extra staff have been brought in to help manually check-in passengers, but it is a slow process.

"There's sketchy information at this point in time. We understand it's a server issue, some sort of communication issue," he said.

"We're looking into that with all our suppliers just to isolate what it is and get it up and running as soon as possible.

"At this point in time, we're told we can have the system up and running within the next hour or two but that's pending receiving more information from our suppliers."

About 800 Virgin passengers are stuck at the Brisbane domestic terminal as all of the airline's domestic and international flights are delayed.

And Adelaide passengers have also been affected by the failure. Virgin says staff are having to use manual check-in and boarding procedures, which is causing delays for both departing and arriving flights.

Sydney Airport says there was also a temporary computer glitch affecting Jetstar operations, but this was ironed out quickly.

It is understood the problem has not affected those flights.

End in sight

The lines for check-in are snaking throughout the Sydney terminal, out the front door and into the taxi waiting area.

There are announcements coming every few minutes, with staff apologising for the delays.

Staff are handing out bag check tags, with passengers being asked to fill out their own cards.

There are around a dozen police officers patrolling the terminal.

One passenger, Doris, was supposed to fly to Adelaide at 8:30am.

"There's been announcements but no time as to when we could get back," she said.

Danielle Keighery from Virgin Blue Corporate Affairs says the system is expected to be back online shortly.

She says customers arriving at the airport now face delays of three or four hours.

Virgin says it will compensate passengers caught up the in massive delays.