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Supreme Court of Canada nominee Marc Nadon, left, arrives to testify before an all-party committee to review his nomination with Justice Minister Peter MacKay in Ottawa on Oct. 2, 2013.CHRIS WATTIE/Reuters

One day after being sworn in, Justice Marc Nadon has stepped aside temporarily from his duties at the Supreme Court of Canada in the face of an unprecedented legal challenge to his appointment from Toronto lawyer Rocco Galati. It is believed to be the first time a Supreme Court judge has stood down before, in effect, sitting down.

The move "throws the Supreme Court into disarray at the beginning of a very big term," said Adam Dodek, a University of Ottawa law professor. Next month, the court is to hear a reference case on Senate reform that includes a question about the possible abolition of Parliament's Upper House. If Justice Nadon is unavailable, the court would probably hear the case with seven members instead of the full nine.

By stepping aside, Justice Nadon deprives Prime Minister Stephen Harper of the bench he sought to create for this week, when a national-security case involving terrorism suspect Mohamed Harkat reaches the country's most influential court. Justice Nadon, in a terrorism case involving Omar Khadr, was a passionate voice for the government's position.

Mr. Galati contends that Justice Nadon was not eligible to take a vacant Quebec seat on the Supreme Court. Section 6 of the Supreme Court Act says a judge on the Quebec Court of Appeal or Superior Court, or from among that province's lawyers, may sit in one of the court's three chairs reserved for Quebec judges. It does not mention the Federal Court.

"The composition of all the courts should be in accordance with the statute and the Constitution," Mr. Galati said in an interview, explaining why he filed a notice of application in Federal Court in an attempt to put the appointment on hold while he seeks a permanent order against it.

He has long been a thorn in the side of Federal Court judges – and Justice Nadon has spent the past 10 years on the Federal Court of Appeal.

Two years ago, Mr. Galati brought about an end to the Federal Court's practice of using former superior-court judges older than 75, the mandatory retirement age, to hear cases at the request of the court's chief justice. The Federal Court of Appeal upheld his challenge. (Justice Nadon was not involved in that case.)

Hugo Cyr, a law professor at the University of Quebec at Montreal, said the Harper government clearly anticipated the possibility of a challenge, as it showed by asking Ian Binnie, a retired Supreme Court judge from Ontario, to look into the legal questions surrounding an appointment from the Federal Court. Mr. Binnie reported that such an appointment is legal. It would not make practical sense, he said, to ask a judge from that bench to resign, then rejoin the Quebec bar for a day or two to qualify. Another retired Supreme Court judge, Louise Charron, and constitutional expert Peter Hogg, affirmed that opinion.

Citing those findings, Paloma Aguilar, press secretary to Justice Minister Peter MacKay, said the government will "defend the rights of Quebeckers who are appointed to the Federal Court to also sit on the highest court in Canada."

Justice Nadon, 64, practised law for 20 years in Quebec and was a judge on the Federal Court's two divisions for another 20.

Mr. Galati argues in his court filing that the government should have referred the issue to the Supreme Court for a ruling on the legality of the appointment.

Prof. Cyr said the decision to step aside is "sad for Justice Nadon," but wise because "no judge wants to have his legitimacy questioned when he hands in decisions."