The appointment marks the second time in two years that Harper has filled a Quebec-designated seat with a male appointment, once again raising questions about why he hasn't done more to address the so-called gender imbalance on the country's highest court.
Nadon's appointment, which will likely be approved, would maintain a ratio of six men to three women on the high court.
Harper faced criticism last year when he appointed Quebec jurist Richard Wagner to the high court instead of a female candidate. Wagner replaced former justice Marie Deschamps.
Nadon's nomination comes after the mandatory retirement of former justice Morris Fish this past August.
Harper will have a chance to address the gender balance next year when Justice Louis LeBel reaches the mandatory retirement age of 75, requiring yet another appointment.
That will mark a complete turnover of Quebec's representation on the Supreme Court; three of the high court's nine seats are reserved for the province.
Harper said Nadon was the best, most qualified candidate for the job.
"His nomination is the result of an extensive review process that included consultations with prominent members of the legal community in Quebec," the prime minister said in a statement.
Nadon is, among other things, a recognized expert in maritime law. His selection by Harper comes after an all-party panel of MPs gave the prime minister a short list of three qualified candidates.
Nadon wrote a dissent in the Federal Court of Appeal's split decision in the Omar Khadr case. Nadon sided with the Harper government and wrote that "Canada has taken all necessary means at its disposal to protect Mr. Khadr during the whole period of his detention at Guantanamo Bay."
Nadon was overruled by two fellow jurists who ordered the government to request Khadr's repatriation from the much-maligned U.S. military prison in Cuba. Khadr has since been brought to a Canadian prison but not before the government faced repeated criticism for not acting.
Nadon is expected to testify before a House of Commons committee prior to the start of the fall sitting of the court, set for next week.
Some legal observers had been expecting Harper to appoint a woman in order to even out the high court's gender balance.
NDP leader Tom Mulcair walked the fine line Monday between praising Nadon as a worthy addition to the country's highest court while recognizing the lack of overall female representation on it.
"This is the highest court in the land. And that has to reflect the population. Now, in 2013, to have twice as many men as women shows some inequality in terms of representation," Mulcair said.
"We're asking the government to be more careful in future in terms of the male-female representation on the court."
Nadon has sat on the Federal Court of Appeal since 2001 after being appointed to the court's trial division in 1993. He graduated from the University of Sherbrooke in 1973 and was called to the Quebec bar at year later. He worked two decades for a large Montreal law firm before becoming a judge.
Harper has now appointed five Supreme Court justices, following the same pattern he adopted in 2006: consulting a five-member committee of MPs, including three Conservatives and one each from the Liberals and NDP.
Nadon was one of three candidates on a list that was presented to Harper. The candidates were not ranked, and the names of the other two on the shortlist were not disclosed.
It was not known if any women's names were on Harper's list. Mulcair refused to address that issue directly, citing the confidentiality of the nomination process.
"We're talking about appointments from a list. When you appoint someone, then that is done by someone who has to look at the composition of the court."
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