The optics are awful.

Whatever the reason for the Canada Revenue Agency’s sudden interest in some of the country’s best-known environmental groups, Prime Minister Stephen Harper’s energy-friendly Conservative government can’t escape the suspicion that it is harassing them to get them to tone down their criticism of the Alberta oilsands, pipelines and other projects that fuel climate change.

As the Star’s environment writer Raveena Aulakh reports, the CRA is auditing some of Canada’s most high-profile and highly respected organizations. They include the David Suzuki Foundation, Tides Canada, Environmental Defence, the Pembina Foundation, Equiterre and the Ecology Action Centre.

“There are enough out there for us to be concerned about this focus,” Marcel Lauzière told the Star. He’s president of Imagine Canada, an umbrella organization for charities. “There’s a big chill out there with what charities can and cannot do,” he told CBC News.

Given the concern this sweep is generating, National Revenue Minister Kerry-Lynne Findlay owes Parliament and the public an explanation for the seeming crackdown. Yet when New Democrat revenue critic Murray Rankin demanded on Monday to know why the government is “trying to intimidate” groups who don’t agree with its policies, she brushed off the question by saying the tax agency “is doing its job,” at arms-length and free from political interference. Far from looking like routine “random selection” audits, these look targeted. The opposition should press for more convincing answers.

As reported by Aulakh, several of the groups being audited believe they have been singled out because of complaints by Ethical Oil, a pro-oilsands group started by Alykhan Velshi, who now works in the Prime Minister’s Office. Green groups say Ethical Oil is funded by the oil and gas industry to counter their activities.

At best, CRA’s focus on critics of the government looks suspicious and raises questions about the agency’s impartiality; that can only hurt its credibility.

This big green chill isn’t new. In 2012 Finance Minister Jim Flaherty’s budget gave the CRA $8 million to focus on charities to see whether they are using more than 10 per cent of their revenues for political advocacy or activity (though not partisan activity, which is prohibited). Flaherty has warned charities to “be cautious” about using charitable, tax-receipted money for political purposes. And Natural Resources Minister Joe Oliver has complained specifically about “environmental and other radical groups” undermining the national interest.

Some might be tempted to shrug at the CRA’s green-prying eyes. After all, if a charity is playing by the rules there’s no risk of its status being lifted. The taxpayers who donate $9 billion or so to charities deserve to know that their money isn’t being put to unapproved uses. In its 2012-2013 report to Parliament the CRA says it audited almost 800 of Canada’s nearly 88,000 charities and revoked the status of more than 1,500. But audits, especially when they focus on a charity’s advocacy activity, can be chilling.

They can distract a charity’s staff from their other roles, such as lobbying to curb climate change, or to protect the air we breathe, the water we drink and the food we eat. A costly audit can also eat into a charity’s resources by imposing heavy paperwork. And any audit that finds fault or levies a sanction, however minor, can tarnish a charity’s image and invite donors think twice before contributing.

One way a charity can protect itself is to mute its criticism of government policy. If it isn’t spending anything like 10 per cent of its resources on political advocacy or activity it isn’t likely to attract complaints, or attention. But that would leave us all the poorer.

Canadians need to hear from alternative, science-based voices as well as from the well-heeled energy industry, as our policy-makers search for the optimal mix of resource development and environmental protection. The Harper Tories may have little taste for a spirited debate, but no one should be cowed into silence.

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