Brisbane and Cooloongatta airports are among those that will be affected when Community and Public Sector Union members stage a two-hour strike at airports and seaports across the country between 9am and 11am.

Australian Customs and Border Protection Service deputy chief executive Michael Outram said travellers should allow extra time when arriving and departing at international terminals.

"Critical border security functions will be maintained during the protected industrial action," Mr Outram said.

"The health, safety and security of the public and our staff continue to be our priority.

"We are working closely with our partner agencies to minimise impacts on operations."

He said anyone booked on international flights within the strike period on Wednesday should allow plenty of time to clear customs.

The strike is the second round of industrial action taken by CPSU employees as they fight Federal Government plans to cut allowances.

CPSU national secretary Nadine Flood said customs and immigration officers would be hit particularly hard by the bargaining policy.

"Customs officers are angry because many of them face losing $5000 to $8000 a year, while small groups of highly specialised officers stand to lose even more," she said.

"Many workers are desperately worried about how they'll pay their bills.

"At the same time, Immigration officers will now be expected to perform many of the tasks that Customs officers do, but without access to the same allowances.

"Border protection 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."