Federal Health Minister Leona Aglukkaq, who sits on the council and is an Inuk herself, says Canada is concerned about the move and has joined other members in "expressing their concern."
"Canadian officials will continue to monitor the situation closely," she told The Canadian Press on Thursday.
"Canada and other Arctic states have requested that Russia and (the Russian Association of Indigenous People of the North) co-operate closely to resolve the situation."
The Russian government surprised Arctic officials from the council's eight member states this week when that country's Ministry of Justice suspended the operations of the Russian indigenous group. The group represents more than 250,000 northerners and is one of six organizations that stand for aboriginals on the council. Canada begins a two-year term as the council's head in the spring.
Aboriginal representation has been a hallmark of the council since it began and remains central to its operation. The "permanent participants" don't have votes, but have full consultation rights and are part of all discussions.
But for the first time in the council's history, the Russian aboriginal group's seat was empty at meetings this week in Haparanda, Sweden.
Duane Smith, head of the Inuit Circumpolar Conference Canada and a council delegate, said from Sweden that the move isn't good news.
"Any time the rights and the roles and the responsibilities of an indigenous organization like that can be impeded concerns ICC," he said.
Smith said the Russian ambassador to the council also seemed surprised. Anton Vasiliev even signed the council's statement of concern.
Michael Byers, an Arctic expert at the University of British Columbia, suggests the move against the Russian group reflects a split in how that government's officials think they should deal with the world. One group supports a centralized, authoritarian approach and one supports more openness.
"The fact that the Ministry of Foreign Affairs was surprised by this and was willing to come out against it says to me this matter has not been resolved with the Russian government," Byers said.
"Ultimately, it will be (President) Vladimir Putin who decides on this. On the one hand, he is exercising more control over dissent within Russia. But on the other hand, he has been a very public proponent of co-operation with other Arctic countries and that includes the Arctic Council."
Rob Huebert of the University of Calgary's Centre of Military and Strategic Studies agrees that the confusing suspension is probably the result of a clash between the Russian government's desire for tighter control at home and its need to co-operate abroad.
But that won't make it any easier for Canada to lead the Arctic Council, he said.
"All of a sudden we've got a huge curve ball about the role of the permanent participants. This is all of a sudden a brand new challenge that Canada is going to have to face."
Smith said he and representatives of the other aboriginal groups just want Russia to sort things out — and quickly.
"We'd just like to see the matter resolved as soon as possible so that (the Russian group) can come back to the table."