The retirement of nine judges in 12 months has put huge pressure on the court that deals with family law matters, including domestic violence.
Chief Judge John Pascoe said in the Federal Circuit Court's annual report 15 per cent of the judiciary had retired in 2014/15 and not all of them had been replaced.
"These delays in appointments have had a significant effect on the court's capacity to deal with matters expeditiously, and waiting times for trials have increased significantly," he wrote.
The court's migration caseload has almost quadrupled over the past five years, to 3900 cases in the past year.
New laws to deal with unprocessed protection claims are expected to result in "an unprecedented volume of work", Judge Pascoe said.
"This workload cannot be met with the current judicial resourcing," he said.
The court not only deals with family and migration matters but bankruptcy, consumer, human rights, intellectual property and industrial issues.
Independent MP Andrew Wilkie says it's not good enough to have families wait an average three years to have a case heard.
"They are often in very dangerous or problematic situations," he said.
"I am told that judges are struggling to cope with the increased demand and that the situation is taking its toll on them both mentally and physically."
The court had an 11 per cent staff turnover rate over the year.
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