Travellers using Australia's major airports on Wednesday morning have been warned to expect disruption as Customs and Immigration officials escalate their campaign of industrial action.

The Australian Border Force faces a tough first day on the job with much of the government's new flagship agency's workforce planning to show up for work two hours late.

Customs and Immigration public servants, whose departments formally merge on Wednesday, are planning half-day strike action as part of their ongoing pay dispute with the Abbott government.

Disruption is expected at airports around the country with Sydney, Melbourne, Brisbane, Gold Coast, Cairns, Adelaide, Perth and Darwin all likely to be affected.

A work stoppage by Customs officers at Melbourne last week resulted in some delays to travellers and on the other side of the country, strike action forced the closure of Customs House in Perth, according to the Community and Public Sector Union.

But the CPSU is escalating its campaign and calling for all its members in the two agencies, except those doing vital national security work, to join in the stoppage.

Feelings are running high in Customs in particular as officers face the loss of the allowances and entitlements that make up much of their pay with the union complaining that some of their members face a $25,000 hit to their annual wages.

There was a partial backdown from departmental bosses last week when they agreed that some of the allowances and entitlements could be carried over into the new entity formed on Wednesday, pending the agreement of a new enterprise agreement for the 13,000 strong merged department.

The CPSU claimed the move as a victory but says it is not enough.

"By standing together, joining our union in huge numbers and participating actively in industrial action, CPSU members in DIBP and ACBPS have achieved a significant win," the union said in a bulletin to members.

"But it's only a temporary stay of execution.

"The government needs to change their policy so we can secure an agreement that maintains Customs and Immigration pay and conditions."

The union's National Secretary Nadine Flood kept up the fighting rhetoric on Tuesday, alleging the Coalition government was leading a push to strip away the wages of its new border force.

"The men and women of the new Australian Border Force will have demanding, dirty and dangerous jobs," Ms Flood said.

"They will be literally putting their lives on the line to keep Australia safe, yet the Abbott Government continues to push a policy that will dramatically cut their take home pay.

"Australian Border Force workers feel disrespected.

"They have been left with no choice but to take strike action to show the Abbott Government they are serious about protecting their rights, conditions and take home pay."

Departmental senior executive Michael Outram said "contingency measures" were in place to minimise disruption, but acknowledged that delays for travellers could not be ruled out.

"While there will be some delays in services, we anticipate that contingency measures in place will keep interruptions to a minimum," Mr Outram said.

"The portfolio regrets any inconvenience this industrial action may cause the public and industry."