"There are review processes in place for the Canada Revenue Agency that have been there for many years, long predating this government," Harper told the House of Commons on Monday.
"These are not political decisions or political matters."
The prime minister was reacting to a CBC News report that the CRA issued a formal letter to the Kitchener-Waterloo Field Naturalists, a charitable group in Ontario, warning that their website contains political material that could violate regulations.
In the Commons, Opposition Leader Tom Mulcair asked when the prime minister had decided "that bird watchers were enemies of the Canadian government?"
"Is this the epitome of the prime minister's social agenda, that he is worried about anyone else talking about the birds and the bees?"
The Harper government ordered the Canada Revenue Agency in 2012 to launch a program to closely scrutinize the political activities of charitable groups, and some 52 audits have begun since.
Many of the groups have challenged government policies, prompting critics to say the audits have been politically motivated to silence opposition.
New Democrat MP Murray Rankin, the party’s revenue critic, said the government is concentrating on birdwatchers while "the real tax cheats are laughing all the way to their offshore banks."
"When will the minister put a halt to her relentless campaign against charities and start focusing on the real tax cheats?"
Revenue Minister Kerry-Lynne reiterated that CRA audits occur free from any political interference, and accused the opposition of trying to score cheap political points.
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