The calls come after figures showed flights between Canberra and Sydney topped the nation for cancellations last month, at 8.1 per cent and ahead of Sydney to Melbourne flights at 7.5 per cent and Melbourne to Sydney at 7.4 per cent.

Department of Infrastructure and Regional Development statistics showed there were 59 cancelled flights on both the Canberra to Sydney route and Sydney to Canberra, far higher than the 30 cancellations between Canberra and Melbourne in the same period.

Canberra Airport managing director Stephen Byron has approached Transport Minister Darren Chester calling for action.

"It's my view that there ought to be a national standard at which the federal government properly investigates the issue," he said.

"That should probably be a level of about 4 to 5 per cent of cancellation rate.

"Sadly that's about the rate that Canberra to Sydney normally rates at, but of course now we're seeing a rate of double that at 8.1 per cent.

"Clearly there needs to be some sort of investigation to find out why Canberra to Sydney is always worse than other routes of out Canberra."

In September, Qantas cancelled 32 flights from Sydney to Canberra, 6.8 per cent of its schedule for the month, while Virgin cancelled 27 flights, or 10.5 per cent.

Qantas cancelled 31 flights in the other direction, or 6.6 per cent, while Virgin cancelled 28 flights, or 10.9 per cent of its schedule.

Nationally, cancellations represented 2.7 per cent of all scheduled flights, up from 1.7 per cent a month earlier and above the long term average of 1.4 per cent.

Mr Byron said the route was previously the 12th busiest in Australia for passenger numbers, but had slipped to 16th.

Passenger numbers between the two cities have fallen 12 per cent since 2009-10, while most capital cities have grown by as much as 15 per cent.

Airlines face stiff competition from driving options and almost 1 million bus trips.

"As an industry, we need to work together to improve the performance of the flights between Canberra and Sydney," he said.

"I do think it's having an impact on the number of passengers. People have said to me the bus is more reliable. They have to contend with Sydney's roads and they still think the bus is a better option," Mr Byron said.

Qantas crews at Sydney Airport told ticket holders last week the repeated delays for flights to Canberra were caused by staffing shortages and competing priorities on other routes.

The airline is increasing use of 737 aircraft on Canberra routes and aims to re-book passengers from cancelled flights within 30 minutes to three hours.

A Qantas spokeswoman said the cancellations were caused by a range of factors.

"Like all airlines, from time to time we experience disruptions due to weather or for maintenance or operational reasons.

"We are very mindful that delays are frustrating for our customers so our teams work hard to minimise the inconvenience, including putting on larger aircraft to get passengers on their way."

Mr Byron said the federal government should consider the poor results.

"The government's role is to protect consumers, customers, from a certain level of badness.

"We should be held to account by the government for this result and we should be asked to come up with the solutions," he said.