Public servants who voted have supported the new deal with a 96 per cent "yes" result after the main public sector union recommended they accept the offer.

The agreement will come after previous votes rejecting offers, unprecendented industrial action, and bitter negotiations.

Community and Public Sector Union deputy national president Rupert Evans described the result as a "bloody nose" for the Coalition government's workplace bargaining rules, but said the deal was far from perfect.

He said it included wage increases of 5.5 per cent to all employees within 18 months, which was still a cut in real terms compared to inflation given Federal Court employees had not received a pay rise in four years.

The Home Affairs Department and the Bureau of Meteorology are among the last of larger agencies yet to reach a new workplace deal, while staff at the Australian Institute of Aboriginal and Torres Strait Islander Studies also rejected a recent offer.

The Federal Court's new agreement would improve working hours, and offered better redundancy and redeployment entitlements to most staff, Mr Evans said.

“The four-year-long process to reach this agreement is a damning indictment on the Turnbull government’s ideological workplace bargaining policy, which wasted huge resources over four years in an effort to cut the wages and conditions of thousands of workers,” he said.

“As a result of the tenacity, commitment and hard work of our members, we were able to reach a point where the union could, on balance, recommend that staff support this agreement."

The union said the deal, endorsed in the vote involving 78 per cent of the staff, followed 43 rounds of protected industrial action. Staff took unprecedented strike action, and heaped pressure on management by handing open letters to people using the courts explaining their rejection of proposed deals.

The Federal Court's staff rejected an offer in June last year after a 90 per cent "no" vote to an agreement that offered an average pay rise of 1 per cent for each of three years, cuts to conditions and entitlements and, for some, a longer working week.

In November, they voted down the proposed enterprise agreement 69 per cent to 31 per cent.

Strikes during the impasse caused significant disruption in the courts by forcing registries to close and delaying hearings.

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

The Federal Court was approached for comment.