That raises a big question mark over what happens to the $1.9 billion tied to the original bill, which has been in limbo since last spring when chiefs from across Canada flatly rejected its proposed reforms to First Nations education.
In a wide-ranging interview with The Canadian Press, Perry Bellegarde said he asked Harper on Jan. 28 not to "re-profile" the money — in other words, not to use funds set aside for First Nations education in last year's budget for another purpose, such as paying down the deficit to balance the books in an election year.
Bellegarde said he did not leave his meeting with the prime minister with a sense of optimism about the education money.
"I can't say yes or no. I didn't get a warm, fuzzy feeling in terms of the request," Bellegarde said Monday.
"So it's a work in progress. But we're not going to quit our efforts. We're going to continue our lobby efforts. It's just too important."
Bellegarde warned of the message it would send to First Nations if the government decides to re-profile the education money.
"It would signal that they're not in touch with communities, not in touch with the needs, and basically putting First Nations issues to the side when it comes to education, which is a travesty," he said.
A spokesman for the prime minister was not immediately available for comment.
The Conservatives' legislation deeply divided the aboriginal community and precipitated the abrupt departure of Shawn Atleo as national chief of the AFN.
Some saw the Conservative bill as a first step — with a substantial dollar amount attached — that could improve the lives of First Nations children. Others viewed it as the government exerting too much control over aboriginal education.
The Conservatives have said the bill will remain on hold and no new money will be spent until the AFN gets behind the legislation.
It appears the AFN is unlikely to do so.
"Bill C-33 will not be going forward," Bellegarde said. "That's where it rests."
So, what then?
Bellegarde is awaiting the outcome of a long First Nations battle at the Canadian Human Rights Tribunal to get aboriginal children in the hands of the state the same level of funding from the federal government as non-aboriginal kids get from the provinces.
If the tribunal's decision — which Bellegarde expects "fairly soon" — on First Nations child welfare is in favour of the AFN and advocate Cindy Blackstock, the national chief said it could also boost the legal argument for more funding for education.
"You can't do the political lobbying, if that's not giving any teeth or any support going forward, then you look at the legal option," he said.
"So that's what has to happen. Then you've got a federal election coming up. You make things a political issue."
The Liberals called on the Conservatives to make the money tied to the education bill available now.
"It's time for the prime minister to stop playing politics with the futures of First Nations children by holding back essential funding for their education," Liberal aboriginal affairs critic Carolyn Bennett said in a statement. "The additional funding for First Nations education announced last year should flow immediately."
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