Travellers heading overseas on Thursday have been warned to expect delays after Customs and Border Protection employees today ruled on a 24-hour strike.

The stop work will affect airports including Sydney, Melbourne and Perth, as well as ports, international mail centre, and container examinations.

"This will have an impact on our operations and could mean delays at international airports for people travelling to or from Australia," Customs and Border Protection Acting Deputy CEO Jan Dorrington said.

"If you have an international flight on Thursday you should go to the airport early and proceed to Customs and Immigration processing as quickly as possible,' she said.

She also warned those travelling on cruise ships arriving and departing from the Overseas Passenger Terminal at Circular Quay should also be prepared for delays.

"The additional delay, while regrettable, is necessary to ensure that the security of our borders is maintained," Ms Dorrington said.

She said Customs and Border Protection has carefully planned contingency arrangements in place, with a particular focus on the Commonwealth Heads of Government Meeting in Perth.

"We have put contingencies in place to protect Australia's border and reduce disruptions to business operations," she said.

"These arrangements worked well during the previous industrial action. In partnership with other border agencies, and the airports and airlines, disruption to operations was minimised.

"We believe these arrangements will enable us to manage CHOGM participants and general passenger arrivals and departures."

The protected industrial action relates to the negotiation of an enterprise agreement for Customs and Border Protection employees.

It comes on the back of news that Jetstar cancelled more domestic flights than Qantas last month, despite the Flying Kangaroo being hit by ongoing strikes.

But Qantas had the highest number of late-running planes, with just over 80 percent of domestic flights departing on time.

A report from the Bureau of Infrastructure, Transport and Regional Economics shows Jetstar cancelled 2.1 percent of flights in September, while Qantas cancelled 1.8 percent.

The first major Qantas disruptions began on September 20, when more than 4,000 Qantas baggage handlers and ground staff stopped work for four hours as part of an ongoing row over pay and conditions.

Virgin Australia had the most on time departures amongst the other major domestic carriers, with nearly 86 percent of departures on time.

It cancelled 1.7 percent of domestic flights.

Tiger Airways, which returned to the skies on a reduced schedule in August after a six-week absence, is showing signs it is lifting its game.

More than 91 percent of its flights arrived on time in September and there were no cancellations.

But it only flew 530 sectors in September, compared to 1,577 the same month the previous year.

The airline was previously grounded because of Civil Aviation Safety Authority concerns after pilots flew too low into Melbourne airports on two occasions, as well as wider safety issues it had previously told the airline to address.

Jetstar blamed single runway operations in Sydney and bad weather for its delays.

The report also showed the route between Newcastle and Melbourne was the worst in Australia when it came to flight cancellations.

Nearly 6 percent of flights from Melbourne to Newcastle were cancelled in September and more than 5 percent on the reverse route.

Melbourne to Sydney was the second worst, with 4.7 percent of flights cancelled.

Overall, on time performance averaged 83.2 percent for on time departures and 82.7 percent for arrivals - slightly more than the same time last year.

Regional Express had the best on time performance of the participating regional airlines, with 87.5 percent of departures on time.