The Congress of Aboriginal Peoples and the Native Women's Association of Canada have written to the premiers to complain about being left out of discussions prior to next week's first ministers meeting.
The letter, obtained by The Canadian Press, expresses surprise and "great disappointment" at the lack of an invitation from Prime Minister Justin Trudeau.
It also calls on the premiers to hold Trudeau accountable to his promise of inclusion.
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"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 the government's decision does not make sense to him.
"In talking to some of the premiers, they're ... shocked at it," Dorey said in an interview. "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 NWAC.
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 Métis 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 provide a specific explanation on why The Congress of Aboriginal Peoples and the Native Women's Association were not invited.
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."'