The Prime Minister's Office is rejecting a call from Canada's legal community to clarify its statement about the Supreme Court, leaving unresolved an allegation that the Chief Justice behaved improperly.

The unprecedented dispute comes as the country's top court prepares for additional constitutional challenges to laws that were passed by the Conservative government. The court agreed last month to hear a case dealing with mandatory minimum sentences for illegal gun possession, while another Conservative law forcing criminals to pay a victim surcharge fee has been flouted by some judges and may reach the Supreme Court.

Fred Headon, president of the Canadian Bar Association, said on Sunday that he is concerned the recent comments from the PMO could undermine the public's faith in Canada's judicial system and called for Prime Minister Stephen Harper to clarify the matter publicly. Those comments come from a statement issued by the PMO Thursday night suggesting that Chief Justice Beverley McLachlin had improperly tried to contact the Prime Minister regarding the government's decision to appoint Justice Marc Nadon to the Supreme Court.

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A separate statement from the Chief Justice's office said the contact between her office and the Prime Minister's Office had occurred during the selection process last summer – when candidates were being considered for the Supreme Court but before anyone had been chosen.

Mr. Headon said it does not appear as though the Chief Justice acted improperly when she flagged a potential issue during the appointment process. "We would like the government to say that the comments they have made should not have been interpreted as if the [Chief Justice] did anything wrong," Mr. Headon said. The Bar Association represents 37,000 lawyers and judges.

The Advocates' Society, an association that promotes professionalism in the justice system, issued an open letter to the Prime Minister on Sunday calling comments from the PMO "unfounded and regrettable" and urged the Prime Minister to publicly correct the record.

Asked on Sunday if the PMO planned to clarify its earlier statement in light of concerns raised by the legal community, a spokesman for Mr. Harper indicated that it does not. "For the record, the statement was issued in response to media queries," Jason MacDonald wrote in an e-mail. "I have no additional comment."

The dispute came to light after the National Post asked the Chief Justice to respond to an allegation – reportedly from senior Conservatives – that she had lobbied against Justice Nadon's appointment.

The Chief Justice's office denied that she had done so in a statement that was later shared with other reporters, and the PMO subsequently issued a statement of its own, indicating the Chief Justice had contacted the Minister of Justice, who then advised the Prime Minister not to take a phone call from her because doing so would be "inadvisable and inappropriate."

The PMO statement prompted another response from the Chief Justice's office, explaining that the contact with the Justice Minister and the PMO occurred in April and July of 2013 – well before Justice Nadon was selected to fill a vacant seat at the Supreme Court.

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Dennis Baker, a political scientist at the University of Guelph, said he believes it is possible that the Chief Justice made a minor error by trying to contact the Prime Minister after she was consulted by the committee responsible for selecting the next Supreme Court justice and after she had flagged a potential issue to the Justice Minister.

"If you repeat a warning – and you are the one who ultimately decides the issue – such warnings can easily take on a different character," he said.

However, Prof. Baker added that such a mistake – if it was a mistake – is very minor and occurred with enough grey area to be defensible. "It surely does not warrant the prominence and attention the [Prime Minister] seems to want to draw to it," he said.