The outage hit the Advanced Passenger Processing system, which is used during check-in to confirm whether a passenger is authorised to travel to their destination, Melbourne Airport's head of communications Grant Smith said.

The system crashed about 8am, forcing airlines to check passengers in manually and causing departure delays on international flights of up to an hour.

The passport system was restored at Sydney and Melbourne airports just before 11am. By midday, it appeared most flights were departing on time.

Earlier in the day, international flights had been departing up to 45 minutes behind schedule from Melbourne and about 30 minutes behind schedule from Sydney, according to the airports' flight listings.

Photos taken at Sydney and Melbourne airports showed extensive queues as passengers waited to check in with luggage.

One passenger at Melbourne Airport told Fairfax Media that by 10am on Monday she had been waiting for about 50 minutes to check in. The line was "crawling" forward, she said.

Passengers have been advised to check with their airlines for potential delays.

The Department of Immigration and Border Protection, which runs the passport system, said it was aware of an "external system outage".

The system went down in New Zealand as well but has now been fixed, the Stuff website reports.