Conservation groups are calling on the federal government to live up to its mandate to protect and restore Fraser River sockeye salmon stocks, by shifting effort and funding back to science and conservation rather than promoting and funding industries like aquaculture.

The demand is being made as part of a series of recommendations submitted to the Cohen Commission, the national inquiry into sockeye salmon declines in the Fraser River that is now in its final stages.

Ecojustice, which is representing a handful of conservation organizations, filed our final submission to Justice Bruce Cohen on Monday. The recommendations come after more than a year of oral hearings, technical and policy reports, and close to 2,000 exhibits. The inquiry is now reaching the last phase of drafting a final report with recommendations to the federal government.

“It’s clear from the tremendous amount of evidence gathered in this inquiry that the government has the mandate and tools to conserve and recover Fraser sockeye,” said Tim Leadem, staff lawyer at Ecojustice. “Fully implementing existing policies, like the Wild Salmon Policy and ‘no net loss’ habitat policy, would put the government back on track.”

Yesterday, as we prepared to file our submissions, news broke that wild sockeye in British Columbia’s Rivers Inlets have tested positive for a flu-like virus that has proven fatal to Atlantic salmon stocks and decimated Chilean fish farms.

It is unclear at this point how the virus, known as infectious salmon anemia or ISA, might affect salmon on the West Coast, but given its track record and the unpredictability of recent wild salmon runs there is reason for concern.

“The only plausible source of this virus is fish farms,” Simon Fraser University fisheries statistician Rick Routledge told the Vancouver Sun.

One critical component of our final submission is a call to remove open net-cage fish farms from along sockeye migration routes. Other key recommendations include limiting fishing rates on endangered stocks and adopting a comprehensive research program, to focus on the cumulative impacts of temperature, habitat loss and chemical contaminants on salmon and their habitat.

We will present our final submission in an oral argument beginning Nov. 4 in Vancouver.

Justice Cohen’s final report is expected to be released in June 2012.

The federal government created the Commission in response to 2009’s dramatic decline in sockeye stocks. More than 11 million sockeye were expected to return to the Fraser that summer, but less than two million arrived.