Federal Court will this week walk off the job for the third time.

The CPSU says the Federal Court, Family Court, Federal Circuit Courts and the National Native Title Tribunal can expect staff shortages as the strike action ramps up.

Community and Public Sector Union deputy national president Rupert Evans says it has been four years since court staff saw their last pay increase, and now face cuts to workplace rights and conditions under EBA proposals.

Court registries in Darwin, Adelaide and Melbourne were closed as workers walked off the job during strikes earlier this month.

“CPSU members in courts feel they have no other option but protected industrial action,” Mr Evans said.

“Courts management refuses to hear workers' concerns about the cuts, they've been through mergers, job losses and more changes are planned.

“Staff have been put through the wringer and enough is enough.

“All federal public servants have struggled to get a fair deal under the Turnbull government's harsh bargaining policy, but in other agencies across the APS we have managed to get the fairest deals possible while fighting off cuts to rights and conditions.

“Not so in courts. Management there is doing everything in their power to treat courts workers like poor cousins. That's why staff are taking this unprecedented industrial action,” he said.

Negotiations are focused on a single agreement for staff following the Federal Court of Australia's merger of administration with the Family Court and Federal Circuit Court last year.

A proposal in June offering half the wage rises being paid to counterparts in other departments and agencies was rejected with a 90 per cent “no” vote in June.

Court staff have been offered an average pay rise of 1 per cent for each of the proposed agreement's three years, combined with cuts to conditions and entitlements and a longer working week for some.