Community and Public Sector Union members working for the department will stop work for four hours during morning and evening shifts to protest against the Abbott government's attempt to cut their pay and conditions.

Union national secretary Nadine Flood said workers were facing losses up to $8000 a year in allowances from their take home pay.

The allowances compensate workers for long hours, unusual shifts, dangerous work and weeks spent away from family.

Workers from the Agriculture Department's quarantine section will also take action along with the Australian Border Force marine unit which will impose bans on loading and unloading stores at ports.

The union says workers in national security, counter-terrorism and specialist biosecurity hazard role won't participate in the industrial action.

AAP