But the government is still reviewing the decision about Nadon's eligibility, which Harper admitted Tuesday left him "very surprised."
"What I can tell you is this: we're obviously going to respect the decision," Harper told a news conference following the conclusion of the two-day Nuclear Security Summit in The Hague.
"We'll respect not just the letter of the decision. We will respect the spirit of the decision as well."
The Supreme Court concluded that Nadon, a semi-retired Federal Court of Appeal judge, does not meet the specific eligibility requirements for a Quebec seat on the bench as spelled out in the Supreme Court Act.
The high court also says the government needs a constitutional amendment to change the criteria for judges on the top court.
The government expected the Supreme Court to find in its favour, because the possibility of a rejection had been characterized by the experts it consulted as "very hypothetical."
"We had commissioned expert opinion on it which was completely contrary to the decision," Harper said.
"But, look, that said, that's the decision. We're still examining the decision. We haven't taken a decision on who the candidate will be. We haven't even taken a decision on taking a decision on the process."
Nadon himself spoke up Tuesday for the first time since the high court's decision, telling Global News in an interview that he was prepared for the court to rule either way.
"I've been living in limbo, you know, since October, so at least this has certainly ended the uncertainty," Nadon said.
He also said he's not sure if he will be required to repay the salary he has earned since his appointment was announced in October. Supreme Court justices are paid $351,700 a year.
"It's the government's decision, so we shall see," he said.
Justin Trudeau was unequivocal on that issue Tuesday, saying Nadon should not be on the hook for what the Liberal leader characterized as Harper's mistake.
"It is certainly not him who asked for this mess. It is ... something the prime minister is responsible for, because of his lack of judgment," Trudeau said.
"I think that to demand from this man, who has enormously suffered because of the lack of judgment of the prime minister, to pay back (his salary) is probably not necessary."
On Monday, Justice Minister Peter MacKay told the House of Commons there are a number of qualified Quebec candidates who could be appointed to the Supreme Court. But he stopped short of ruling Nadon out entirely.
That left opposition MPs expressing concern that the government would continue to push for Nadon's appointment — a fear NDP Leader Tom Mulcair couldn't quite let go, despite Harper's promise to respect the decision.
"As long as I don't hear the minister of justice or the prime minister say that in no way will they come back with Marc Nadon, I fear that they are reckless enough to come back with Marc Nadon," Mulcair said.
When the government originally sought a legal opinion last summer on Nadon's eligibility, it asked retired Supreme Court judge Ian Binnie two questions: whether Nadon was eligible as a Federal Court judge and, if he was not, whether he could simply be readmitted to the Quebec bar for a day to become eligible.
Binnie opined that Nadon was eligible for appointment as a member of the Federal Court of Appeal, then declined to answer the second question.
Binnie wrote that "any hypothesis that requires of a person who starts the week as a Federal Court judge to rejoin the Quebec bar mid-week for a day or two in order to 'qualify' for appointment to the Supreme Court by the end of the week makes no sense."
"Such a two-step expedient," Binnie added, "is neither required nor compatible with the dignity of the office being filled, in my opinion."
Nadon told Global he has not applied to the Quebec bar and said he would resume his work at the Federal Court of Appeal.
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