Chief Justice Debra Mortimer on Friday issued a statement backing Mordecai "Mordy" Bromberg in the high-profile position.
She sidelined media commentary that suggested he was not fit to serve as commissioner due to appeals against his judicial rulings.
"The suggestion that mere reversal signifies anything about the competence of the trial judge subject to the appeal, is as misconceived as it is unfair," she said in a statement.
Justice Bromberg's judgments were cited often in court and "reveal the application of a keen intellect to the judicial task".
"The court rejects out of hand any idea that Justice Bromberg has not at all times discharged his office in accordance with his judicial oath and likewise emphatically deprecates the insinuation to the contrary," the chief justice said.
Justice Bromberg was this week appointed by federal Attorney-General Mark Dreyfus to lead the commission for the next five years.
The former St Kilda AFL player and one-time Labor candidate has hit the headlines previously over his rulings, including finding News Corp columnist Andrew Bolt had breached section 18C of the Racial Discrimination Act in 2011.
That decision sparked repeated efforts by conservative politicians to strike out the section.
Justice Bromberg made the decision to allow the Biloela Tamil family to remain in Australia until a full court hearing was held on their case.
He was also behind a 2021 decision that the federal government had a duty of care to young people to prevent climate change, later overturned on appeal.
The appeal outcome included that government policy should not be run by the courts.
Chief Justice Mortimer said all judges face ruling reversals and the media coverage questioning Justice Bromberg's competence was wrong.
Her statement was an unusual step, with courts normally steering clear of formally commenting on media coverage and public issues.