Guy Pratte's resignation comes after he filed a motion last week with the Federal Court arguing that the Canadian Judicial Council panel hearing the inquiry had over-stepped its bounds by becoming involved in a hearing while also presiding over it.
Pratte did not immediately return calls seeking comment and the executive director of the council would not say why Pratte stepped down.
"I am not going to comment on why he left. We are aware of course of the judicial review application and it is something that the council may have to address at some point," Norman Sabourin said Monday.
"We have accepted that resignation and we have to move forward to make sure it doesn't create a delay."
A council committee is looking into the conduct of Justice Lori Douglas, whose husband uploaded sexually explicit photos of her to the Internet in 2003, when the couple were family law lawyers at a Winnipeg firm.
Douglas eventually went on to be named associate chief justice of the Manitoba Court of Queen's Bench, heading up the family court division.
Earlier this month, Douglas's lawyer asked the Federal Court to quash the inquiry.
Sheila Block argued that, during cross-examination of some witnesses, the lawyer acting for the committee members, George Macintosh, had used "aggressive and argumentative questions, sexist and insulting references, misstatements and distortions of the evidence and attacks on (Douglas's) character and credibility''.
Pratte filed his own application with the court. He did not ask that the inquiry be scrubbed, only that Macintosh be prevented from asking any more questions and that previous questions be stricken from the record.
"The procedure adopted by the committee is beyond its jurisdiction, violates the (Canadian Judicial Council) bylaws and policies and ... is inconsistent with the principles of fairness by which the committee is legally bound," Pratte wrote.
The committee, which includes the chief justices of Alberta, Prince Edward Island and Newfoundland and Labrador, disagreed.
"An inquiry committee retains a responsibility to search for the truth. It is performing a vital fact-finding mission," the committee members wrote in a document released last week.
"If that requires an inquiry committee, directly or through its counsel, to engage in strong questioning of a witness, then this necessity must prevail over any perception of the moment."
The controversy around Douglas began when her husband, Jack King, sexually harassed a client.
In 2003, when Douglas and King were family law lawyers at the same firm, King uploaded sexually explicit photos of Douglas on a website dedicated to interracial sex. Some showed her in bondage gear or performing sex acts. He also emailed photos to a client named Alexander Chapman and asked him to have sex with Douglas.
Chapman complained to the law firm and King settled the matter within weeks by paying Chapman $25,000 to return all the photos and to never discuss the matter.
Chapman broke that deal in 2010 and complained to the judicial council, insisting Douglas was part of the sexual harassment.
Among the allegations before the inquiry is that Douglas did not disclose the matter when she applied to be a judge. She applied three times before finally being accepted in 2005.
The inquiry is also examining whether the very existence of the photos precludes Douglas from continuing in her job.
Douglas has said all along that her husband acted without her knowledge and that she should not be punished for her husband's misdeeds. She and King are still married.
Macintosh grilled Douglas's husband last month, suggesting it was impossible that Douglas never knew about the nude photos. With rapid-fire questions, he repeatedly asked King how Douglas could not be alarmed that he had snapped more than 100 pictures of her over the years, with digital, film and instant cameras.
It's not clear when Block or Pratte's applications to the Federal Court might be heard. The inquiry is on a break. It was originally scheduled to finish hearing evidence last month, but most witnesses have yet to testify. The committee had talked about resuming hearings in the fall, although no firm dates have been set.
The Canadian Judicial Council has only held inquiries into judges nine times in 40 years. It has only once recommended that a judge be removed.
In 2009, the council recommended to the federal government that Paul Cosgrove be removed as a justice of the Ontario Superior Court due to incompetence and abuse of his powers. Cosgrove resigned before the federal government could make its decision.