Eskasoni First Nation Chief Leroy Denny said the reserve's fishermen were previously taxed on the income they earned from the commercial fishery.
But after nearly five years of negotiations, the federal agency has told the First Nation that fishermen in the Cape Breton community will no longer be taxed, said Denny.
"The fishermen and their families are very happy and relieved," Denny said of the more than 100 fishermen in Eskasoni. "It's good for the Mi'kmaq community in general. ... It's quite a victory for us."
In 1999, a Supreme Court of Canada decision found that Mi'kmaq have the right to catch and sell fish to provide a moderate livelihood for their families.
In that case, Mi'kmaq Donald Marshall launched a legal challenge after being charged in 1993 with fishing eels out of season, fishing without a license and trying to sell illegally caught eels.
Max Faille, a national leader for aboriginal law with Gowlings law firm in Ottawa, said following the decision, the Eskasoni fishermen assumed that their income would be tax exempt and challenged the agency when it was not.
"This is something that they felt all along was correct and it had pretty devastating implications for them, particularly when people saw that a lot of their other benefits were being clawed back by (the Canada Revenue Agency)," said Faille from Ottawa on Saturday, pointing to child tax benefits.
"People have been waiting patiently for this outcome."
In February, a dozen Mi'kmaq communities, including Eskasoni, filed a notice of application with the Nova Scotia Supreme Court alleging that Canada has not met its obligation to accommodate fishing treaty rights.
Denny said he hopes the latest ruling from the agency will open up more discussion with government about fishing treaty rights.