Thousands of airline passengers are facing delays, including families heading off for the school holidays, following an air traffic control system failure in Sydney.

Dozens of flights have been cancelled while many more are experiencing delays of more than two hours.

One pilot described the Harbour City's skies as being "like a ghost town" to air traffic control as he came in to land.

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Air Services Australia (ASA) said there had been a "system software failure" at Sydney's air traffic control at 5:00am.

As a result, only a limited number of flights were able to land and depart.

ASA said the glitch had now been resolved but the airlines expected disruptions to continue as they dealt with a massive backlog.

There are long queues at check-in and transfer desks.

ABC News obtained a radio exchange from one plane landing at Kingsford Smith — normally the country's busiest airport — this morning.

Controller: "Betcha never seen this place so quiet on a Monday morning." Pilot: "Like a ghost town."

Sienna Excell, 13, is missing the start of her holiday to Queensland's Heron Island. ( ABC News: Lexy Hamilton-Smith )

Passengers are facing delays of up to three hours while others are having to wait until tomorrow morning to board a flight.

Some of the major airlines expect to put on additional services to ease the disruptions.

Jan Ibbottson is on holidays from the UK and said it was frustrating her flight to the Gold Coast was cancelled.

"I'm very calm about it, but it's chaos," she said.

Ms Ibbottson said the airlines had not handled the situation well.

About 15 planes can land and depart per hour using manual air traffic control methods, but there are usually about 50 movements per hour.

ABC journalist Lexy Hamilton-Smith's 7:30am flight from Sydney to Brisbane was delayed.

She said passengers have spent more than an hour on board QF506 while the plane waits on the tarmac, but only passengers with no check-in baggage have been allowed to get off.

Passengers on board delayed QF506 were told they could not get off the plane if they had checked baggage. ( ABC News: Lexy Hamilton-Smith )

Kay Wallace from Bunbury in Western Australia is in Sydney attempting to get to Hobart for the 50th anniversary of the Hash House Harriers social running club.

Her flight from Perth to Melbourne overnight was cancelled and she was put on a flight to Sydney.

"The backlog here has to be cleared before we can even look like going to Hobart," Ms Wallace said.

The ABC understands the fault relates to the flight planning system.

There were long delays at Sydney Airport on Monday. ( Twitter: @NadineFloodCPSU / ABC News: Mark Reddie )

This feeds into the radar picture and without it, controllers cannot see which plane is which.

It is also believed the data connection between Sydney and Melbourne was down.

The Qantas departure board lists flights to Melbourne, Brisbane and Adelaide "delayed due ATC Radar Failure".

Passengers have been urged to contact their airlines.

Passengers face long delays at Qantas Domestic Transfer following an air traffic control system failure. ( ABC News: David Spicer )

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