Prime Minister Justin Trudeau is under pressure from the premiers to ensure that the Congress of Aboriginal Peoples and the Native Women's Association of Canada are included in discussions next week ahead of the first ministers' meeting in Vancouver.
Manitoba Premier Greg Selinger said the premiers had a brief discussion and believe all five national aboriginal organizations should attend.
Selinger's comments come after the two excluded groups sent a strongly worded letter of complaint to the premiers.
"We've had that tradition in the past when they meet with the Council of the Federation," Selinger said in an interview with The Canadian Press.
"We meet with all five organizations and we're supportive of continuing that practice."
The premiers don't see any reason why the groups cannot attend, Selinger added.
"There is some good leadership there," he said. "We just want them to be heard and part of the process."
The letter to the premiers, obtained by The Canadian Press, expresses surprise and "great disappointment" at the lack of an invitation from Trudeau.
It also calls on the premiers to hold Trudeau accountable to his promise of inclusion.
"At a meeting held on Dec. 16, 2015, the prime minister reiterated the federal government's commitment to include all five (national aboriginal organizations) in high-level discussions pertaining to indigenous issues," it reads.
"It is extremely important that all indigenous voices are heard and not just a select few."
Dwight Dorey, the national chief of the Congress of Aboriginal Peoples, which represents about 1.1 million indigenous people living off-reserve, said Tuesday the government's decision does not make sense to him.
"In talking to some of the premiers, they're ... shocked at it," Dorey said.
"It is clearly discrimination. It goes totally against the commitment that the prime minister made."
Dorey said he's seeking the support of the premiers in the hope it will convince Trudeau to invite both the congress and the women's association.
In a statement, the Prime Minister's Office said Trudeau would meet the premiers, the Assembly of First Nations, the Inuit Tapiriit Kanatami and the Metis National Council ahead of the first ministers meeting "in the context of a renewed nation-to-nation relationship."
The meetings do not in any way preclude ongoing discussions with all five national aboriginal organizations, as committed to by the prime minister late last year, the statement said.
"The government of Canada has committed to working and meeting regularly with the national aboriginal organizations and will continue to engage in robust bilateral discussions with all five ... on issues of importance to their members," said spokesperson Andree-Lyne Halle.
Halle did not explain why the congress and the association were excluded.
NDP indigenous affairs critic Charlie Angus said he is still trying to figure out what the government is trying to accomplish by leaving out the two groups.
"Mr. Trudeau said he was going to end Stephen Harper's standard operating practice of picking winners and losers and creating confrontation by excluding people he didn't want to hear from," Angus said.
"The message they're sending is, 'There are going to be winners and losers with this new government'."
With files from Chinta Puxley