Harper says those values that are loathed by many employees of CBC's French-language network are the same ones that he says are supported by a large number of Quebecers.
Harper made the comments during a French-language interview with Quebec City radio station FM93, conducted last Friday and aired today.
His remarks were described as "petty" by an NDP MP.
Harper's comments about Radio-Canada came in response to a question about how he plans to convince Quebecers to vote for his party in the upcoming federal election.
He says he doesn't believe that voters in Quebec are predominantly left-leaning.
Rather, he says, Quebecers approve of the measures taken by his government: lowering taxes, staying tough on crime and cracking down on the threat of terrorism.
"I remain convinced that Quebecers are not leftists, contrary to the image conveyed by some media or the opposition parties," Harper says in the interview.
"I understand that there are many at Radio-Canada who hate these values, but I think that these values are the true values of a large percentage of Quebecers."
NDP labour critic Alexandre Boulerice said it's clear Harper and his party dislike the public broadcaster.
"I think Mr. Harper's comments are absolutely deplorable and shows the whole ideology of the Conservatives, who don't like Radio-Canada," Boulerice said in Ottawa.
"I think Prime Minister Harper and the Conservatives have had a negative bias towards Radio-Canada and this for a long time."
The Conservatives hold just five seats in the province, compared to seven for the Liberals and 54 for the New Democrats.
It wouldn't be the first time the Conservatives have attacked Radio-Canada.
In February 2011, Jason Kenney accused the broadcaster of "lying all the time" in response to a question from a journalist.
More recently, Harper's spokesman Carl Vallee wrote that it was becoming "more and more difficult for (him) not to conclude that (his) worst suspicions about Radio-Canada held true."
Vallee was reacting to a documentary aired last year about the religious right in Canada which explored links between evangelical Christian groups and the Harper government.
Radio-Canada ombudsman Pierre Tourangeau concluded in that case that standards governing the presentation of journalistic views were not properly applied.
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