The creation of Australian Border Force (ABF) is placing "horrendous" pressure on staff and leading to long delays at Melbourne Airport, the union representing ABF airport officers says.

The Community and Public Sector Union (CPSU) said the merger of the customs and immigration departments into the ABF had resulted in fewer staff rostered on the frontline.

National Secretary of the CPSU Nadine Flood said the culture at ABF was causing problems, citing the bungled joint Operation Fortitude, which had to be cancelled after confusion over whether people would be forced to show their immigration papers in Melbourne's CBD.

"There are just some real problems there, as we saw in Melbourne a few weeks ago," she said.

"We have seen passenger numbers double in the last 10 years [at Melbourne Airport] but with this merger now, there are less staff rostered on the front line.

"There still seems to be an awful lot of Border Force bosses in Canberra and there are real pressures.

"So Melbourne Airport is relying on overtime and administrative staff being pulled onto the primary line, there's higher levels of sick leave and staff are saying 'we just can't do any more overtime'."

Passengers have complained of sometimes waiting hours for to be processed after landing at Melbourne Airport on international flights.

Ms Flood said delays would increase, not just in Melbourne but across the country, with industrial action planned for next week as part of an ongoing pay dispute.

"There are already pressure points, and we are looking at further strike action, there will be strike action nationally at international airports next week, every morning and night for a two-hour stoppage," she said.

"That is going to have an impact, but these workers are in an 18-month long dispute and they still face cuts to their current take-home pay.

"We may see significant delays with strike action at Melbourne Airport and other airports, and obviously over the weekend as the picture becomes clearer ... we'll provide as much advice to the travelling public as we can."

The problems at Melbourne Airport come as Victoria Police's chief commissioner Graham Ashton suspended joint operations with ABF after the Operation Fortitude bungle.

Border Force working to improve delays

The ABF said in a statement Melbourne Airport had experienced significant growth in traveller numbers in the past two years and they were working to improve service at the airport.

"The ABF works closely with other border agencies as well as with the airport operator to improve the traveller experience when moving through Melbourne Airport," the statement read.

"The ABF's efforts to improve passenger flows need to be balanced with our obligation to ensure the protection of the border."

It said the introduction of new technology, including self-processing gates which are due to come on line in October, would improve the situation at Melbourne Airport.

"The ABF has a transformation program that will introduce high levels of automation and technology, resulting in a seamless, low-touch experience for passengers in Australia's international airports," the ABF said.