But a pathologist at the B.C. agriculture ministry says the study is based on incomplete data.
The paper published in the journal Ecological Applications argues that in the past decade, salmon farmers began treating their fish with a product known as SLICE, an anti-parasitic chemical, in the fall and winter months. As a result, researchers have found fewer sea lice in coastal waters around the Broughton Archipelago.
The timing of the treatments is important because it means in the spring, when juvenile pink salmon travel to the sea through the archipelago, the sea lice numbers have dropped. The fish are most susceptible to the parasites at that time.
The research team, led by Stephanie Peacock, a PhD student, found mortality rates for juvenile pink salmon fell to less than four per cent by 2009.
Listed as co-authors of the study were Martin Krkošek of New Zealand's University of Otago, as well as Stan Proboszcz and Craig Orr, who are both members of the Watershed Watch Salmon Society, and Mark A. Lewis, who is Peacock's academic supervisor.
Peacock said the data used in the paper dates back to 2001 and was provided by well-known but controversial industry critic Alexandra Morton. Peacock said researchers also used data from the salmon-farming industry found in other publications.
She said juvenile pink salmon are susceptible to the effects of sea lice because the parasites are free living and can be swept out of open net-pen enclosures and into the path of wild fish.
A media release sent out by the university said sea lice had a devastating effect on wild juvenile salmon in the early 2000s, "killing an estimated 90 per cent" of the young fish after natural threats and associated mortality.
"This paper is important because it reiterates the fact that sea lice negatively impact wild-salmon survival," Peacock said in an interview.
"But the new aspect is that adaptive changes to farm management can reduce sea-lice outbreaks and allow pink salmon in the Broughton Archipelago to begin recovery."
Gary Marty, a fish pathologist for B.C.'s Ministry of Agriculture, said he doesn't dispute that the SLICE treatments and their timing are important.
But he said the paper's researchers base their conclusions on the belief that sea lice numbers are harmful to wild salmon, and Marty questioned whether that's a given.
He said the researchers considered data between 2001 and 2009, but did not take into account data from 2000.
"We found that the second highest number of sea lice ever that we know of in the Broughton occurred in 2000. That was on fish farms. But in 2001, the pink salmon came back in record high numbers," Marty said.
He said the new paper doesn't even analyze those high sea-lice levels or returns.
"I think we all agree that the SLICE treatments, when they're co-ordinated, they're very effective in British Columbia in decreasing the sea-lice numbers on the farmed fish, and that's also very effective in decreasing sea lice on the wild fish," he said.
"What we disagree about is how many lice were on the farms in the 1990s and 2000, and then what the effect of those lice are."
Peacock said she stands by her paper, noting the data she used was published by Marty and also found in another academic journal.