Passengers stranded at Melbourne Airport

Virgin Blue has begun the complicated task of getting about 6000 stranded passengers onto flights in Melbourne after a computer breakdown.

A damaged cable under Melbourne airport brought down the airline's telecommunications service provider, crippling its passenger check-in process from lunchtime on Tuesday and forcing the cancellation of 48 flights.

"Telstra rectified the problem at 10.30pm (AEDT) last night so we can access our systems and that's all back on track," said Virgin Blue spokeswoman Amanda Bolger.

"We anticipate some delays today with the flow-on impact of the flights that were cancelled."

More flights were cancelled on Wednesday with pilots and crew members also left stranded overnight and unable to get to cities they were supposed to fly out of.

Hundreds of passengers had to be provided with accommodation overnight and thousands of meal vouchers were provided, Ms Bolger said.

"We have flown in extra staff and had others doing double shifts," she said.

"We will get back on track as quickly as possible but are dealing with a huge number of passengers."

Passengers had to be checked in and boarded manually on Tuesday, creating a massive delay and a huge backlog.

All domestic destinations were affected but trips to Sydney were worst hit.

- AAP