During the 1998 pilot project, the federal Department of Fisheries and Oceans allowed three aboriginal bands a 24-hour salmon fishery on the river while non-native fishermen remained at the dock.
In a decision released Friday, the high court justices ruled 9-0 that the federal government was within its rights to give the First Nations a head start on the commercial fishing season while excluding non-natives.
The decision upheld the convictions of more than 50 non-native fishermen who defied the department, and set their nets for sockeye salmon during the window reserved for the aboriginals.
While the B.C. provincial court originally stayed the charges on the grounds that the special fishery violated the charter rights of the non-native fishermen, that decision was overturned on appeal and they were convicted of illegal fishing.
The Supreme Court agreed with the B.C. Court of Appeal and held that the special fishery for natives was an attempt to help a disadvantaged group, which is expressly allowed under section 15 (2) of the charter.
Chief Justice Beverley McLachlin and Justice Rosalie Abella wrote that the exclusive fishery fell under the part of the charter that essentially allows affirmative-action programs.
The non-natives couldn't claim a violation of their rights, they said.
"The claim of discrimination must fail," the judgment said.
The First Nations Summit, which represents aboriginal bands involved in the B.C. treaty process, said the decision recognizes the right of the federal government to try to provide economic opportunity to aboriginals.
"This decision clearly reaffirms First Nations' rights to fish and provide for their families," Grand Chief Ed John said in a statement issued Friday.
John said the ruling recognizes the purpose of the pilot program.
And he said it's a compelling reason for the federal fisheries department to renew the program, which was cancelled following the heated confrontations on the water a decade ago.
"The government's aim was to address the indisputable 'disadvantage of aboriginal people...' rooted in history and which continues today," John said.