Senior public servants in the Department of Fisheries and Oceans are worried the department has lost the ability to keep track of salmon species other than sockeye – including the chinook critical to the survival of the endangered southern resident killer whale.

In the July letter, a copy of which was obtained by The Globe and Mail, area directors in B.C. expressed “collective concerns with the continued under-resourcing of salmon stock assessment programs.”

Area directors wrote that they appreciate that under-resourcing is not simply because of reduced science funding in recent years, but the result of “eroded regional funding” from various sources over the past 15 years.

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“The regional ability to meet well-established core salmon assessment programs is no longer possible with allocated funding,” said the letter.

Recently, there have been concerns about dismal returns for chinook salmon on the Fraser River, raising new concerns for the endangered southern resident killer whales that rely on these fish for their survival.

The perilous state of the whales was also a significant factor in the decision by the Federal Court of Appeal on Aug. 30 to halt the Trans Mountain pipeline expansion project.

Carmel Lowe, the regional science director for the department, was the recipient of the letter. She said since the letter was written, the department has committed to spending an extra $4-million on its monitoring responsibilities. That would bring its budget this year up to approximately $11.2-million for salmon stock assessment, about $1-million more than in each of the past four years.

“We have secured or anticipate having secured the funding required to allow all of the priority assessment programs to be undertaken,” Ms. Lowe said.

In an e-mail exchange subsequent to the interview, Ms. Lowe said internal and external sources of funds for salmon stock assessment have varied over the years, with declines in, for example, Pacific Salmon Treaty implementation funds, but increases in other sources of funding such as for implementing the recommendations of the Cohen Commission of Inquiry into the Decline of Sockeye Salmon in the Fraser River.

Still, the letter makes plain that the authors are concerned about dwindling resources over more than a dozen years, combined with increasing responsibilities.

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Ms. Lowe said the department lacks the resources to “go out and assess every fish,” but, rather prioritizes. That means a focus on Fraser River sockeye, given Indigenous interest in the fish and their higher market value, and chinook given the dependence of killer whales on them.

In May, the federal government announced a reduction of roughly one third in the harvest of chinook and closured fishing in some key whale foraging areas after declaring that the southern resident killer whales face an imminent threat to their survival. The federal government has acknowledged that lack of prey is one of the critical factors affecting the whales' recovery.

A spokesman for the First Nations Fisheries Council of B.C., which works with and on behalf of B.C. First Nations to protect First Nations fisheries rights and title, said he was not surprised by the area directors' letter.

“I think it’s something that those who work with fisheries here in B.C. [have] all expected and known,” council operations manager Janson Wong said in an interview.

The result, he said, is that DFO is often “guessing” about what returns and spawning might be.

“A lack of data means a lack of good management,” Mr. Wong said.

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With report from Justine Hunter in Victoria