Canada's closest allies and neighbours have called for a formal investigation into the government's refusal to offer full protection to polar bears threatened with extinction because of climate change.

The secretariat of the Commission for Environmental Co-operation (CEC) said this week there were "central open questions" about Canada's decision to offer only limited protection to polar bears. The CEC, which was set up by America, Canada, and Mexico under the North America free trade agreement, went on to call for an investigation.

Canadian officials may not have given enough importance to research predicting the loss of two-thirds of the world's polar bears by 2050 due to melting of Arctic sea ice, the secretariat suggested. The 2007 study by US Geological Survey researchers said a number of polar bear populations inside Canada would disappear entirely, or be severely decimated.

Partly in response to that work, America declared polar bears an endangered species in 2008, but Canada stopped short, listing polar bears as a "species of special concern" in 2011.

This week's recommendations from the CEC secretariat, in response to a petition from the Centre for Biological Diversity, further underlined the Canadian government's international isolation over its environmental policies. The Centre for Global Development this week ranked Canada last among the world's 27 richest countries for its environmental record.

Canada has also come under strong criticism at the international climate negotiations in Warsaw this week for expanding the carbon-heavy Alberta tar sands and dropping out of the Kyoto protocol.

Meanwhile, the prime minister, Stephen Harper, has been accused of weakening environmental regulations and "muzzling" government scientists who do not fit in with his energy agenda.

"This is a government that believes first of all that economic development, particularly resource extraction, is substantially more important than environmental protection and environmental stewardship," said Chris Turner, whose book, The War on Science, charts the government's clashes with scientists.

Now, in a further rebuff to the Canadian government, it appears even the neighbours have doubts about its environmental stewardship.

"The secretariat finds that there remain central open questions about Canada's enforcement of the Species at Risk Act, in respect of the polar bear species," said the CEC.

It went on to call for an investigation leading to the publication of a "factual record" tracing the key steps in Canada's decision to deny top tier protection to a critically at risk species. The secretariat has given the CEC council 60 days to respond.

In calling for the investigation, the secretariat said it was unclear whether Canada had based its decision on the "best available" science. The Canadian government this week defended its 2011 decision, saying the polar bears were protected under "strong domestic legislation to conserve and protect wildlife in Canada".

Sara Uhlemann, the senior attorney who pursued the Centre for Biological Diversity's case, said that determination was critical.

"The most critical part of this is really questioning the science by which Canada made its decision to refuse protections to polar bear," she said. "It says there are open questions as to whether Canada was looking at best climate science out there and that the climate science is very clear."

She said the designation offered little in the way of real protection. "If you are listed as that third category as a species of special concern you really don't get any special protection," she said.