The prime minister says Robert Abdallah was proposed by the city and the federal government went along.
Harper insisted Abdallah, the former city manager for Montreal, wasn't a federal nominee.
Abdallah was accused at the Quebec corruption inquiry this week day of being part of an elaborate kickback scheme involving construction firms.
Abdallah never got the Port job and he has denied he ever took kickbacks.
Harper distanced himself from the man during a brief news conference with reporters on Thursday.
"First of all, it's very important to say that Mr. Abdallah was never an employee or agent of the government of Canada," Harper said.
"For that position, he was proposed by the City of Montreal where he was the city manager and we supported the nomination of the city itself."
In 2006, the year that Abdallah left the city government, his name began circulating as possible president of the Montreal Port Authority.
The chairman of the Port's board has said he and other directors met Dimitri Soudas, then a close aide to Harper, at a Montreal restaurant in the spring of 2007 and Soudas pressed Abdallah's candidacy.
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