Administrative Appeals Tribunal president Justice David Thomas has resigned from the role.
Justice Thomas was appointed president of the tribunal and a judge of the Federal Court of Australia in June 2017.
He will remain as a judge of the Federal Court.
Attorney-General Michaelia Cash said Justice Thomas, who has been on leave, had provided strong leadership at the tribunal.
Federal Court judges Susan Kenny and Berna Collier will act as AAT president.
The tribunal has not been without controversy in recent years, with claims coalition-appointed members had been paid hundreds of thousands of dollars despite failing case finalisation benchmarks.
There have also been concerns about conflicts of interest not properly being disclosed.
The AAT provides independent merits review of a wide range of administrative decisions made by the federal government.
