Thousands of employees of Australia's Customs and Border Protection agency will strike on Tuesday to protest their pay and work conditions.

The industrial action is expected to affect international airports in Sydney, Melbourne, Brisbane, Cairns, Perth and Adelaide as customs employees in airports, ports and mail facilities stop working for one to two hours to attend labor union meetings.

"These staff don't want to go on strike this is very much a last resort but unfortunately they don't feel they have any other option," ABC quoted Community and Public Sector Union National Secretary.

Ms Flood said the impact of the job walk off would depend on the response of air carriers which are expected to send in airline management staff to minimise passenger delay.

The customs workers rejected a 3 per cent pay increase offered by the federal government because the amount offered is not enough for employees to keep pace with spiraling cost of living.

Ms Flood warned of more similar industrial action affecting public service. It comes on the heel of last week's strike by Qantas engineers, baggage handlers, catering staff and ground crew which partly paralyzed operations of the flag carrier.

The customs, border protection and quarantine workers are seeking a 4 per cent salary adjustment, but the federal government has placed a nine percent pay increase cap over three years or 3 per cent annually.

"Customs and Border Protection has negotiated in good faith with all bargaining representatives to propose an agreement that is affordable within its budget and within the parameters of the Australian government bargaining framework," Ms Flood told The Sydney Morning Herald.