The judge who conducted a two-year inquiry into the health of one of British Columbia's most lucrative fisheries has concluded the federal government's changes to the Fisheries Act have the potential to harm -- not help -- Fraser River sockeye.

B.C. Supreme Court Justice Bruce Cohen also said it was "regrettable" the government didn't wait to pass Bill C-38 until after he had submitted his report.

"I find it difficult to avoid the conclusion that legislative amendments in Bill C-38 lower the standard of protection for Fraser River sockeye salmon," he said.

Bill C-38 was tabled five months after Cohen's hearings were over and it was enacted this summer. The bill changes how fish habitats are protected and puts in place new management enforcement and environmental assessment provisions.

Cohen said his biggest worry is that those changes are focused more on developing fisheries than promoting habitat, even though experts have stressed eco-based values such as promoting biodiversity.

He said changes to the Fisheries Act might actually authorize harm to fish habitat. They appear to be taking the Department of Fisheries and Oceans in a very different direction than the one he laid out in his report, he said.

"DFO's first priority must be the health of wild stocks." Cohen said repeatedly during the news conference.

"What about the future?" Cohen asked. "I my view, unless significant, remedial measures are introduced soon, the stressors that are currently believed to affect sockeye negatively will continue to do so."

Cohen's report runs more than 1,000 pages and was produced after he spent more than two years investigating why millions of sockeye vanished from the 2009 Fraser River run.

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.

The report didn't come up with a single "smoking gun" that explains why the fish didn't return.

Among the recommendations, Cohen calls 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.

"I therefore conclude that the potential harm posed to Fraser River sockeye salmon from salmon farms is serious or irreversible," he told media after releasing his report on Wednesday.

He said there is a conflict within the Department of Fisheries and Oceans Canada between conservation of wild stocks and promotion of the aquaculture industry.

But Cohen said the most troubling impact on the fish was climate change, and noted that 13 of 20 summers in the region had been the warmest on record.

"I can't think of a greater threat to sockeye than climate change."

"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."

Pitt Meadows-Maple Ridge Conservative MP Randy Kamp, who is the parliamentary secretary for the fisheries minister, said the federal government was reviewing the recommendations.

"I want to assure Canadians that we, like all British Columbians, want to see a sustainable and prosperous salmon fishery for years to come."

During almost a year and a half of hearings, Cohen heard from 160 witnesses, and compiled 14,000 pages of transcripts. There were 2,100 exhibits entered at the inquiry that sat from August 2010 to December 2011.

The inquiry explored everything from aboriginal fishing to aquaculture, commercial fishing to disease, habitat management and enforcement to predation.

The iconic fish has been bandied about as a symbol of everything from government mismanagement, corporate greed and climate change.

One of the most volatile issues has been the aboriginal food fishery versus the commercial salmon fishery. At times, the debate has exploded into violence on the river as fishermen have competed for what seemed an ever-shrinking resource.

The fight between conservation and First Nations groups and the open-ocean aquaculture industry has maintained an almost constant presence in the court of law and the court of public opinion in British Columbia.

The offspring of the 2009 spawning run are expected to return to the Fraser River during the summer of 2013.

Cohen's report was originally due May 1, 2011, but that deadline was extended to June 30, 2012, Sept. 30, 2012, and then finally Oct. 29, 2012.

His recommendations, in any event, were pre-empted by an austere federal budget that cut $79 million -- 5.8 per cent -- from the Fisheries and Oceans Canada budget. In B.C., that will result in closure of all but five federal fisheries field offices and an overall staff reduction.