Australia has confirmed its worst flight cancellation and performance rate since records began.

Figures compiled by the federal government's Bureau of Infrastructure and Transport Research Economics revealed only 63 per cent of Qantas, Virgin, Jetstar and Rex Airlines flights arrived on time in June while just 61.9 per cent departed when scheduled.

It said 5.8 per cent of flights were cancelled, meaning June of this year had the worst on time performance figures since the data started being recorded in November 2003.

The cancellation rate was more than double the long-term average figure of 2.1 per cent.

Qantas fared the worst with 8.1 per cent of its flights cancelled.

That was followed by QantasLink at 7 per cent, Virgin Australia at 5.8 per cent, Jetstar at 5.5 per cent, and Virgin Australia Regional Airlines at 5.3 per cent.

Rex Airlines appeared to be the most reliable last month, with only 0.7 per cent of flights cancelled.

The bureau said the weather and issues relating to COVID-19 contributed to the poor performance.

Qantas said a rise in cases of COVID and other illnesses among airline crew as well as the tight labour market led to flight disruptions for all domestic airlines in June.

The airline said it had rostered additional crew on stand-by to lessen the impact of COVID-related crew absences and said cancellations so far this month were down on those recorded in June.

"Everyone at Qantas and Jetstar is focused on turning this performance around," the spokesperson said.

"We're already seeing improvements and things will continue to get better month-on-month.

"Call centre wait times are now better than they were pre-COVID and our mishandled bag rates are close to what they were before the pandemic."

Virgin Australia echoed the reasons given for the poor performances, saying flights had been significantly affected by weather events in New South Wales as well as resourcing pressures associated with COVID and the large numbers of passengers returning to travel.

"While this result is not where we want to be, this outcome is a result of the extraordinary efforts of our team who continue to work around the clock to help our guests get to their destinations during busy periods," a spokesperson said.

Virgin said it had recently made operational changes which had already reduced the number of flights it needed to cancel this month.

It said its cancellation rate was trending in the right direction and was down to 2.4 per cent this week.

Sydney and Melbourne passengers worst affected

Cancellations by all airlines were highest on flights from Sydney to Melbourne at 15.3 per cent, followed by the Melbourne to Sydney route, at 14.9 per cent.

Flights between Sydney and Canberra, and then the Canberra to Melbourne route were among the next highest to be cancelled.

Melbourne Airport's chief of aviation Jim Parashos said airlines had been working hard to rebuild their workforce after being completely shutdown during the lockdowns of 2020 and 2021.

He said the flu season and Omicron wave hit operations hard, with federal regulations around minimum crewing requirements regularly grounding an entire service.

"In some cases, it could be just one cabin crew being off sick that then results in a flight being cancelled," Mr Parashos said.

Delays hit airports around the country

For the flights that did go ahead in June, punctuality was a problem across the board.

The on time arrival figure of 63 per cent for June was significantly lower than the long-term average of 82.1 per cent.

Similarly, the bureau said the 61.9 per cent departure figure was also significantly lower than the long-term average of 83.3 per cent.

Rex Airlines was the most punctual, recording 80 per cent for on time arrivals, followed by Virgin Australia recording 62.4 per cent.

Jetstar just edged out its parent company Qantas, with a 59.5 per cent result ahead of the latter's 59.1 per cent.

Virgin had the most timely departures, with 60.4 per cent of flights leaving as scheduled.

Alice Springs fared the best for arrivals at 87.2 per cent and Armidale Airport had the most flights leave on time, with 81.5 per cent of flights doing so.

Mildura had the tardiest arrivals with only 47.2 per cent of planes landing on time.

Delays could continue for months

Mr Parashos said airports and airlines were actively recruiting more staff to try to cover illnesses and shortages.

But he said while the hospitality industry could train a new worker in a week, pilots, cabin crew and baggage handlers require more rigorous training to meet regulated standards.

"They're operating in highly sensitive areas, their work is quite often very technical and of course they need security clearances as well so it can take two or three months sometimes to get people of that nature on board," Mr Parashos said.

He said the ramping up of skilled migration would help but it would still be some time before the industry bounced back to pre-pandemic levels.

"We will see improvement in the months ahead, and part of that is the airlines are building a bit more resilience into their networks and scheduling to allow for last minute requirements."

He said Australia was not alone, with the same challenges being faced around the world.