For those managed under the Indian Act, there's a process whereby they can contest an election. The federal government continues to be the one making sure there's an investigation. The minister or delegated authority under the minister conclude if the election was valid or not. In those cases it's Elections Canada.
A lot of first nations choose to get out of the Indian Act for their elections. In their case, it's their own law and rules. As far as I remember, they have to go through court, like anybody else, if they want to contest an election.