Judge Michael Simon said in a ruling issued Friday that the program intended to preserve endangered salmon by killing sea lions is within the bounds of the fisheries service.
"This case is about how Congress, NMFS, and the states have tried to balance the protection of sea lions with the protection of threatened and endangered salmon and steelhead," Simon wrote.
The program was reauthorized last year, through June 2016.
The Humane Society of the United States sued, saying the program targeting sea lions is arbitrary. They say the animals consume, at most, 4 percent of the salmon coming through the Bonneville Dam. Commercial and sport fishers, by contrast, take nearly 17 percent, The Oregonian reported.
Simon said fishery managers can scale back fishing when runs are low but can't do the same for sea lions.
The states of Oregon, Washington and Idaho backed the plan, part of an effort to keep alive five runs of salmon and steelhead listed under the Endangered Species Act that pass Bonneville, the first dam they encounter on the Columbia River.
Under the re-authorization, the states are allowed to kill up to 92 of the animals a year, either by lethal injection or shooting them. They have to be identified as eating salmon and not deterred by hazing efforts.
Barring a successful appeal, the decision means the lethal-take program will resume when the seal lions return to Bonneville this spring. NMFS plans to assess the program again after 2016.
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