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Grand Chief Derek Nepinak of the Assembly of Manitoba Chiefs prepares to speak in Headingley, Man., on June 6, 2013.JOHN WOODS/The Canadian Press

A schism in aboriginal leadership is threatening to divide the Assembly of First Nations as a new alliance moves to convince native communities across Canada to choose its path to sovereignty from federal rule.

Derek Nepinak, the Grand Chief of the Assembly of Manitoba Chiefs, came away from a meeting of the new National Treaty Alliance in Saskatchewan on Thursday saying the members of the group will try to sell First Nations on an "empowered" approach for asserting treaty rights. They will be "asking people to decide, do they want an Indian Act future or do they want a future built on the Treaty Alliance, based on the sovereignty of our people," Mr. Nepinak told The Globe and Mail.

The focus of the Treaty Alliance will be the implementation of existing treaty rights as a way to move First Nations on the path to independence and away from the governance of the 137-year-old law that has become a target of resentment for native people.

To emphasize his point, Mr. Nepinak threw away his Indian card.

The alliance intends to meet again in October to solidify its structure. If all goes according to plan, it would later demand a meeting with Prime Minister Stephen Harper and set a 30-day deadline for a response. If the demand is not met, a campaign of action would be launched.

The meeting of the Treaty Alliance this week at the Onion Lake First Nation was timed to coincide with the annual general meeting of the Assembly of First Nations in Whitehorse. Chiefs and their delegates had to choose which event to attend. The fact that many divided their time between the two meetings, and that both attracted about a thousand delegates, is an indication of the strength and the influence of the startup group.

The organizers of the Onion Lake gathering accuse Shawn Atleo, the National Chief of the AFN, of talking privately with the federal government about issues that could affect treaty negotiations – something Mr. Atleo vehemently denies.

The AFN is an advocacy group that represents the diverse interests of Canada's 614 First Nations but has no authority to negotiate treaties. It also receives operating money from Ottawa.

"The new Treaty Alliance is different," Mr. Nepinak said. "It's not going to rely on government of Canada money. We're not going to be manipulated by bureaucrats and contribution agreements. We're going to do this on our own."

Mr. Atleo, who says the AFN is also committed to moving beyond the Indian Act, has warned that the First Nations are stronger when they work together. In a telephone interview on Thursday, he said that the AFN and the Treaty Alliance did not need to compete and said the goals of both groups are the same.

Some of those attending the Saskatchewan meeting said they did not see the Treaty Alliance as a rival to the AFN but a vehicle for asserting their treaty rights. And the native leaders attending the AFN meeting in Whitehorse sent an open letter Monday to those at Onion Lake, saying they are fully supportive of First Nations driving the implementation of their own treaties.

"We made sure to express to those gathered in Onion Lake at Treaty Six Territory our respect, care and support and we included the word love and said we know we are pushing for the same things," Mr. Atleo said.

The AFN and the Treaty Alliance could work as complementary organizations for the betterment of the First Nations, he said. The question, Mr. Atleo said, is "how do we push in a concurrent manner in a way that is mutually supportive and yet respects the autonomy and diversity and sovereignty nations."

Perry Bellegarde, the AFN Regional Chief for Saskatchewan who attended both meetings, agrees. "People are looking always for that divisiveness," Mr. Bellegarde said. "There are more things that unite us and we've got to focus on those things rather than the things that divide us."

But Mr. Nepinak said he could not speculate about what kind of role the AFN will have going forward.

"I think what we're seeing is a shift or an evolution back to fundamentals that we needed," he said. "And I don't just hold Shawn's leadership responsible for this shift. I think we all own a piece of this and we have to consider the role that Mr. Harper has played in making many people wake up across the land in recognizing that we have to stand up and find new ways to assert our jurisdictions once again."

Separately, the AFN is calling on Mr. Harper to acknowledge the "horrors" of nutritional experiments once done on hungry children by increasing support for native child welfare.

"We're going to call on the Prime Minister to give effect to the words that he spoke when he said: 'The burden of this experience has been on your shoulders for far too long. The burden is properly ours as a government,' " Mr. Atleo said in reference to Mr. Harper's 2008 apology for residential schools.

Recently published historical research says hungry aboriginal children and adults were once used as unwitting subjects in nutritional experiments by Canadian government bureaucrats.

With a report from The Canadian Press