The group, which represents aboriginal people living off-reserve, says it's unfair to people who live outside the remote northern Ontario community to have to cast their vote in person.
Despite the complaint, voting went ahead Tuesday.
"I think it's absolutely ridiculous," Betty Ann Lavallee, national chief of the congress, said in an interview.
"If you looked right now at the costs of an airline ticket to Attawapiskat for the ordinary aboriginal person living off-reserve, you're taking about some of the poorest of the poor here. There's no way they could afford that."
According to Aboriginal Affairs and Northern Development Canada, the Attawapiskat First Nation has a total registered population of 3,472. Of that, 1,489 people — or about 43 per cent — live off-reserve.
Charles Hookimaw is a band member of the Attawapiskat First Nation who lives in North Bay, Ont. He says his concerns about allowing off-reserve band members to vote were ignored.
"This election process, to me it's a non-democratic process," Hookimaw said.
The congress says a 1999 Supreme Court of Canada ruling requires all First Nations holding elections under the Indian Act to give people who live off-reserve the right to vote.
"It's not an accommodation. The court was quite clear that aboriginal people living off-reserve have the right to vote," Lavallee said.
A spokesman for Attawapiskat Chief Theresa Spence was not immediately available to comment.
Spence is seeking re-election after a turbulent tenure in which she gained notoriety for subsisting on fish broth and tea for six weeks as a form of protest during the rise of the Idle No More movement.
The Idle No More cause, which began in December and January, was a protest against the Conservative government's omnibus Bill C-45.
First Nations groups claimed the bill threatened their treaty rights set out in the Constitution.
But Spence's protest also drew unfavourable attention to Attawapiskat with the release of a scathing audit of the band's books that found a missing paper trail for millions of dollars between 2005 and 2011.
The troubled reserve is widely known for the housing crisis that prompted a state of emergency in the winter of 2011 and set off lingering tensions with the federal government.
Flooding and sewer backups this spring again forced Attawapiskat into a state of emergency and forced the First Nation to evacuate its only hospital.
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