In a joint statement arrived at after hours of debate, the two sides acknowledged their relationship has been fraught with problems.
"Unfortunately, there have been low points in our relationship. A series of misguided and harmful government policies in our past has shaken First Nations confidence in our relationship," said the statement.
"We cannot undo the mistakes of the past, but we can learn from them and affirm that they will not be repeated."
The three page joint statement laid out commitments in five areas, including removing barriers to First Nations governance and advancing the implementation of treaties.
But how those shared causes would be advanced wasn't entirely clear.
The Conservative government and First Nations chiefs did agree to set up a working group to review the structure of government financing and also to set up a task force within three months on economic development.
The initiatives spring from a joint action plan the two sides released last June.
Part of that plan had included developing recommendations on improving education on reserves, and while it had been widely believed that Tuesday's talks would lead to an endorsement of new powers for native communities in that area, it wasn't part of the final communique.
Instead, both sides agreed they'd review the eventual report on education and implement those recommendations they could both agree on.
Shawn Atleo, national chief of the Assembly of First Nations, said the discussions Tuesday had touched on every element of First Nations lives and livelihoods, including tapping into a greater share of natural resources wealth.
"The sense is that our work does not end here. This is very much the beginning," Atleo said.
"We wanted to see an expression of commitment not only to this day but that they would be prepared for an ongoing effort with us. They've expressed that willingness to do that."
Both sides have pledged to report back in one year's time on the progress they've made overall.
The date for the talks had been set late last year, as residents of the Northern Ontario reserve of Attawapiskat became poster children for squalid living conditions in many aboriginal communities.
National chiefs had gone into Tuesday's meetings hoping for immediate agreements on how to solve some of those problems, as well as a long-term plan.
But Aboriginal Affairs Minister John Duncan said the gathering did what was intended: strengthen and re-establish the relationship between the two sides.
"One of the important things - you have to offer hope and hope is a great motivator," he said.
The day had began in apparent conflict over the Indian Act, but the two sides managed to close the gap by agreeing that while it can't be immediately repealed, it can be modernized.
Atleo, who earlier in the day led a parade of native speakers pillorying the act, appeared to extend an olive branch to the prime minister by stating it "cannot be replaced overnight."
"We will arrive at a day where the Indian Act is simply obsolete, a relic of the past," said Atleo. "And we can do it. The proof is that some First Nations are already there."
The Indian Act, first passed in 1876, gave Ottawa exclusive jurisdiction over "Indians and Lands Reserved for Indians." The legislation, which was last amended in 2000, defines who is recognized among First Nations and sets out rules on everything from how reserves operate to the effect of marriage on status.
Harper told the gathering the act can be updated to reflect modern practices and while he conceded the act led to problems over the years, but the government has no plans to repeal the legislation.
"After 136 years, that tree has deep roots," he said. "Blowing up the stump would just leave a big hole.
Though there had been fears the prime minister would beat a hasty retreat from Tuesday's meetings, he stayed throughout the day and was seated front row centre for the closing speeches.
It was a small gesture of goodwill that went a long way, said Ghislain Picard, regional chief of the Assembly of First Nations of Quebec and Labrador.
But how far that goodwill extends remains to be seen. Picard said he's not sure he trusts the government.
"Time will tell if this meeting has proven itself to be useful," he said.
"What we have to remind ourselves is we've had six years with this government, and in recent months, especially since this government became a majority government, they've been pushing pieces of legislation where there was no consultation in any way with our people, with our communities, so if that way of doing business doesn't change, obviously the trust will fail to be there."
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