"I think it's appalling that the judiciary should be used for political purposes in this way and I'm puzzled as to the motivation of the prime minister and his office as to why they would take on the chief justice," Gomery said.
Talking to Evan Solomon on CBC Radio's The House, Gomery said he finds the situation 'distasteful' and 'bewildering.'
Last week, the prime minister suggested Chief Justice Beverley McLachlin acted improperly last July when she advised his office that a Federal Court judge might not fit the legal criteria set for Quebec appointees to the Supreme Court.
McLachlin subsequently issued a statement saying all she wanted to ensure was that the government was aware of the eligibility issue.
The Supreme Court later rejected the appointment of Marc Nadon, a Federal Court judge.
"The whole point of it is that [Harper] is assuming that [McLachlin] could somehow — using a crystal ball, I guess — know that he intended to appoint Marc Nadon to the Supreme Court and that she is going to comment on that," Gomery said.
This week, a group of past presidents of the Canadian Bar Association and the Canadian Council of Law Deans both criticized the prime minister's remarks.
Gomery told Solomon that Stephen Harper's approach undermines the independence of the Supreme Court.
"The suggestion that their conduct is inappropriate means that they are, in the eyes of the person accusing them of inappropriate behaviour, behaving in a partisan way," he said. "It's an accusation that the court has become partisan."
The retired Superior Court judge also dismissed the prime minister's concerns when it comes to the impact of the Nadon decision on Quebec judges.
"The idea that there is somehow a shortage of qualified candidates for the Supreme Court is absolute nonsense," he said.
Gomery provided some insight as to why the prime minister may be struggling to fill the vacant Quebec seat on the high court.
"I think the province of Quebec is more liberal, small "L" liberal, than perhaps the rest of Canada and that, I think, makes Mr. Harper uneasy about Quebec judges because they come from that culture, from that milieu, and they are, I think, representative of that opinion," he said. "He's looking for a Conservative judge and it's hard to find one in Quebec because Quebecers are not Conservative in the same way that, should we say, people from Alberta are Conservative."
Gomery was appointed to investigate the sponsorship scandal, which informally became known as the Gomery Inquiry, in 2004.
He retired from the bench in 2007.
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