"We do anticipate a possible flow on effect later today however we encourage passengers to check with their airline for the most up to date information on their particular flight".
By about 9am, air traffic controllers were able to handle 80 flight movements an hour.
The backlog of flights is expected to be cleared by early afternoon.
There were long queues at check-in and transfer desks.
Jan Ibbottson is on holidays from the United Kingdom and said it was frustrating her flight to the Gold Coast was cancelled.
Two officers shot in New Haven, Conn., standoff
An officer ordered the man to drop the item but the man refused and continued to move toward the officers, Moore said. The man seems unaffected when the officer fires the stun gun and quickly rushes toward the officer.
According to News Corp, the universal system used by Air Services Australia has been disrupted.
Ms Ibbottson said the airlines had not handled the situation well.
ABC journalist Lexy Hamilton-Smith's 7.30am flight from Sydney to Brisbane was delayed.
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.
This feeds into the radar picture and without it, controllers can not see which plane is which.
Sydney's terminal was hit by radar failures at about 5am, which also resulted in flight delays for thousands of air travellers south of the NSW border.