It is "regrettable" that the government did not wait to see the conclusions of the inquiry before making changes to the federal Fisheries Act, Cohen told the media Wednesday.
"The amendments to the Fisheries Act cause me concern," Cohen said in a comprehensive 1,000-page report containing 75 recommendations.
"I find it difficult to avoid the conclusion that the legislative amendments in Bill C-38 lower the standard of protection for Fraser River sockeye salmon."
Cohen notes in his report that the legislative changes were tabled five months after hearings ended, as he was writing his draft report.
Contrary to his recommendations to protect salmon habitat, Cohen said the amendments contained in the Conservatives' omnibus budget legislation appear to expand the circumstances where fish habitat can be harmed.
"DFO's first priority must be the health of wild stocks," Cohen said repeatedly during a news conference.
Cohen received more than three million pages of documents, sat through more than 100 days of evidence and listened to almost 900 public submissions.
In the end, he said there was no "smoking gun" to explain the decades-long decline of sockeye, but he pointed to a number of factors both in the immediate habitat of the Fraser River run and in the region.
Contributing factors in the decline include contamination and development along the river and conditions faced by juvenile salmon at sea.
But Cohen said the most troubling factor impacting the fish was climate change, and noted a two-degree increase in water temperatures in the Fraser River over the past 60 years.
"I cannot think of a greater threat to sockeye than climate change," Cohen told reporters. His report notes that Canada has withdrawn from the international Kyoto Protocol to reduce greenhouse gas emissions.
"We should look to the government of Canada for domestic action and for Canadian support and encouragement of international initiatives that will reduce the impact of warming waters on Fraser River sockeye."
Millions of sockeye salmon vanished from the Fraser run. Just 1.4 million sockeye showed up in a run that was anticipated to be around 10 million. The following year, the Fraser River run defied all expectations, coming in at an astounding 30 million.
Among the recommendations, Cohen called for a freeze on the controversial practice of net-pen salmon farming around the Discovery Islands, on B.C.'s central coast, saying salmon farms have the potential to introduce disease to wild salmon. Scientists do not know enough about the risks of salmon farms on wild stocks, he said.
"I therefore conclude that the potential harm posed to Fraser River sockeye salmon from salmon farms is serious or irreversible," said the report.
Cohen also cited a conflict within Fisheries and Oceans Canada between conservation of wild stocks and promotion of the aquaculture industry, and he recommended industry promotion be transferred to another department.
Randy Kamp, the parliamentary secretary to Fisheries Minister Gail Shea, said the federal government was reviewing the recommendations.
"We're just beginning our careful review of the report," Kamp said in Vancouver.
He stressed the report findings that there is no one factor to blame.
"Clearly, as Justice Cohen highlights, this is a complex issue," Kamp said.
The government did not commit to implementing any of the recommendations, and Kamp defended the Fisheries Act changes.
"What we think the amendments to the Fisheries Act ... did is allow us to focus on the protection of the fisheries that Canadians value — commercial, recreational and aboriginal fisheries."
He said "serious harm" is prohibited against those fisheries.
Gwen Barlee, policy director with the Wilderness Committee, disagreed.
The federal government has gutted key tools that protect wild salmon in B.C., she said after listening to Cohen speak.
"You have to wonder, when Justice Cohen is going in one direction calling for better protection of salmon, better science, better habitat protection, the federal government is going in the opposite direction," she said.
Several First Nations groups welcomed the recommendations concerning fish farms.
Chief Bob Chamberlin is with the Kwikwasut'inuxw Haxwa'mis First Nation, a First Nation located in the Broughten Archipelago, an area he described as "ground zero of the fish farm struggle."
"That's something our nation has been advancing and trying to have addressed and accommodated for decades, but has fallen on deaf ears with the government," he said.
Stewart Hawthorn, board member with British Columbian Salmon Farmers Association, said the recommendation for a freeze on salmon farms in the Discovery Islands affects only five of 70 farms in the province.
"What Justice Cohen has said is that he is impressed by the quality and quantity of the data that we have provided to his inquiry, in fact, we were second to none," he said.
"It's a very small part of what we do," he said.