Department of Infrastructure and Regional Development statistics from September showed cancellations were highest on Canberra to Sydney and Sydney to Canberra flights at 8.1 per cent, ahead Sydney to Melbourne flights at 7.5 per cent and Melbourne to Sydney at 7.4 per cent.

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.

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.

The national rate of cancellations was higher than the long term average of 1.4 per cent, the figures showed.

Nationally, airlines Jetstar, Qantas, QantasLink, Regional Express, Tiger, Virgin and Virgin Australia Regional averaged 79.3 per cent for on time arrivals in the month and 80.6 per cent for on time departures.

Frustrated travellers faced three cancelled Qantas flights in three hours on Thursday alone, with frustration added to by weather-related delays in Canberra.

Qantas ground crew at Sydney Airport told ticket holders the repeated delays for flights to the capital were caused by staffing shortages and competing priorities on other routes.

One passenger was told on the phone two cancellations in one day on the Sydney to Canberra route were caused by mechanical issues, before later being told by ground staff it was because Qantas didn't have enough crew members to fly on other routes.

Fairfax Media asked Qantas about the cancellations on Friday morning, but did not receive a response to questions from the airline until Tuesday morning.

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

"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."

A Virgin Australia spokeswoman said there were not ongoing problems on Sydney to Canberra route.

"Cancelling flights is never our preference but unfortunately we do occasionally need to change services due to adverse weather, operational requirements or other factors outside our control.

"We understand this can be frustrating for our guests and we appreciate their patience and understanding," she said.

In the 2016-17 financial year, the routes with the highest cancellation rates included leisure flights between Sydney and Hamilton Island at 5.0 per cent, followed by the Canberra and Sydney and Moranbah and Brisbane routes at 4.6 per cent.

The Sydney to Canberra route had 4.2 per cent cancellations, matched by Sydney to Melbourne, Melbourne to Sydney, Brisbane to Moranbah and Rockhampton to Brisbane routes.

By comparison in September, there were no cancelled flights between Canberra and Adelaide and three between Canberra and Brisbane.

Canberra Airport did not comment on the cancellation rates.