An inquiry into the collapse of the Fraser River sockeye run began Tuesday in Vancouver. (Chuck Stoody/Canadian Press)

An official investigation into the collapse of sockeye salmon stocks in B.C.'s Fraser River is expected to get underway in Vancouver on Tuesday morning.

The Cohen Commission of Inquiry launches the first three days of what is expected to be a lengthy and technical probe into the disappearance of almost 10 million fish from the 2009 Fraser River sockeye run.

Only about one million fish returned to spawn, prompting the federal government to order an investigation led by B.C. Supreme Court Judge Bruce Cohen.

A discussion paper released in advance of this week's hearings indicates the inquiry will examine everything from fish biology to the organization of the Department of Fisheries and Oceans.

One of the most controversial aspects of the inquiry is expected to focus on the role of open-pen fish farms dotting the B.C. coast along wild salmon migration routes.

Critics believe lice and other contaminants from the fish farms are deadly to wild salmon, but the discussion paper says Fraser River sockeye experience a "suite of impacts" which must all be evaluated in order to understand the collapse.

DFO ties raise concern

But one Vancouver-area MP is worried about the impartiality of the Cohen commission. John Cummins, the Conservative MP in Delta-Richmond East, says too many scientists on the panel have ties to the Department of Fisheries and Oceans.

"The last 15 years of management, mismanagement, have been at the hands of the Department of Fisheries and Oceans. And as the structure of this inquiry now stands, all of the information is going to be filtered through this science panel of people who are either ex-bureaucrats at DFO or people whose careers relied on the department," he told CBC Radio on Tuesday morning.

Brian Wallace, the head lawyer for the Cohen commission, said it was impossible to avoid some links to DFO when assembling the commission's experts, but there's a wide range of voices that will provide balance.

"Our hope is to have a broad range of evidence from a number of different expert witnesses to help the commissioner," he said.