Employees of the Federal, Family and Federal Circuit courts and the National Native Title Tribunal voted down the enterprise agreement by 69 per cent to 31 per cent, putting no end in sight to the bitter workplace deadlock that has drawn many staff for the first time into rolling strikes.

The main public sector union vowed more industrial action would follow, while Federal Court executive director Darrin Moy told staff it would accept the Fair Work Commission's offer to mediate in the ongoing battle after the result.

Staff rejected the deal after a 90 per cent 'no' vote in June to an agreement that offered an average pay rise of 1 per cent for each of the three years, cuts to conditions and entitlements and, for some, a longer working week.

In the latest knockback, 980 staff voted down a deal offering a 5 per cent pay rise across three years, but retaining cuts to conditions and entitlements, and forcing a longer working week on some employees.

Staff will remain without a pay rise for four years and continue their battle amid more uncertainty following reports of possible changes that could have the Family Court scrapped and merged with the Federal Court.

The Community and Public Sector Union said the proposed agreement was deeply flawed, and signalled staff would resume strikes and other industrial action from Monday.

CPSU deputy national president Rupert Evans said the result showed Federal Court staff would never accept an agreement that stripped away critical workplace rights and conditions.

"This situation is completely unjust to courts staff, who have gone well over four years without a pay rise and yet are still facing unfair cuts to their workplace rights and conditions. That's on top of the recent mergers, job losses and even more disruptive changes they know are coming.

"These are people who had never taken strike action before this dispute, which underlines how bad this situation is."

Mr Evans said it was a tribute to employees' resolve that Federal Court management belatedly agreed to conciliation through Fair Work.

"But that doesn't change the fact that this isn't going to be resolved until the cuts to existing rights and conditions come off the table."

Staff are negotiating a single agreement after the Federal Court of Australia's merger of administration with the Family Court and Federal Circuit Court in 2016.

Previous strikes have caused significant disruption in the courts by forcing registries to close and delaying hearings.

A courts spokesman said the wages offer put to staff was the maximum allowed under the Coalition's bargaining policy.

"We tried to obtain an exemption from the wages increase cap, however the government did not permit a relaxation of this policy," he said.

The courts also agreed there would be no change to redeployment, redundancy and retention provisions and assured staff that all existing policies would only be changed with consultation as directed by the government's bargaining rules, the spokesman said.

He said the Federal Court had previously told Fair Work that once a result was known it would contact the commission regarding its invitation to mediation.

"This was because bargaining was continuing and management had made a number of concessions regarding its position."