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Jonathan Hill and Elliot Knudsen work on equipment at the Pacific Salmon Commission at their observation outpost in Mission, British Columbia on September 16, 2014.The Globe and Mail

The Fraser River's sockeye run is being hailed as exceptional by fisheries experts even though there is considerable doubt about how many millions of salmon remain at sea and how many of those fish should be caught.

"I would call it a great run," Jennifer Nener, area director for the Department of Fisheries and Oceans (DFO), said Tuesday as seine boats were given a three-day opening to scoop up late-arriving sockeye off the mouth of the Fraser.

The overall run is estimated at 20.7 million fish but a final number can't be calculated yet because of uncertainty about the number of sockeye holding in salt water just off the river's mouth.

Ms. Nener said an estimated three million to six million sockeye are milling about where the north, middle and main arms of the Fraser River spill into the Strait of Georgia.

Until those fish move up into the river and pass an acoustic counting fence near Mission, B.C., fisheries managers won't have a solid read on just how many salmon are in that late-running group.

Because of that doubt, conservationists are calling for caution in fishing the late stages of the run, fearing the commercial fleet might hit stocks too hard.

However, Ms. Nener said the run has been so strong that even if the count for the late-arriving fish is low, there will still be lots of sockeye on the spawning grounds.

"I think right now … things are looking great," she said.

The Fraser has four major "management groups" of sockeye, which arrive in waves through summer and early fall. The first in to the river are the early Stuarts (this year an estimated 233,500 fish) which are followed in order by the early summer run (1.9 million), the summer run (7.8 million) and the late run (10.8 million).

Fisheries managers estimate the size of each of those runs by doing test fisheries and by counting fish at the Mission acoustic fence.

But Ms. Nener said the late run stock is still holding off the mouth, making it difficult to confirm the run size.

"They are still coming in, which is a little bit tricky because the other management groups tend to swim by, get assessed in our test fisheries and then pretty much go straight up the river so we have good correlation between test fisheries and numbers at Mission," she said.

Aaron Hill, of Watershed Watch Salmon Society, said without firm numbers on the late run group, the DFO should be cautious about how much commercial fishing is allowed.

He accused DFO of "taking a very unprecautionary and aggressive approach to fishing. They are fishing much harder than the science … would recommend."

Mr. Hill said if the DFO misjudges the run size it could allow too many fish to get caught.

Ms. Nener disagreed, saying there are "enough buffers built into the system."

Mike Lapointe, chief biologist with the Pacific Salmon Commission, agreed that the overall sockeye run is exceptional this year, although some of the management groups did better than others.

For example, he said the early summer run came in at about two million less than forecast, while the summer run came in at about two million over the forecast.

Mr. Lapointe said although the late run stock is proving difficult to assess, because it is holding at sea much longer than usual, the delay in entering the river could be advantageous, because salmon survive better when the river is colder.

Usually the late run fish are up the river by early September, he said, when the river is several degrees warmer than it is now.

"This run could be the latest in the last 50 years in terms of its upstream migration and that should bode really well for their survival. If we've still got three million out there, and those fish have less than 10 per cent mortality, then you are going to see an abundance of fish on the spawning grounds," he said.

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