SEATTLE - A federal court judge on Wednesday struck down a Bush administration decision to consider hatchery-raised salmon alongside their wild counterparts in determining whether certain runs need Endangered Species Act protection.

U.S. District Judge John C. Coughenour's rulings in two related cases immediately boosted the listing for Upper Columbia River steelhead from threatened to endangered. The rulings also set the stage for a federal appeals court to reconcile differences between his decisions and that of a federal judge in Oregon in 2001.

“The purpose of the Endangered Species Act is to promote populations that are self-sustaining without human interference,” the judge wrote. “If the ESA did not require that species be returned to a state in which they were naturally self-sustaining, preservation of the habitat of the species would be unnecessary.”

Many scientists are concerned that counting hatchery-raised fish in determining the health of a species can mask declines in natural fish stocks, though some argue that hatchery fish can bolster wild populations. Hatchery-raised fish do not have the same survival rates that wild fish do and their prevalence could genetically whitewash the traits that distinct salmon runs developed over the millennia.

The legal dispute arose following a 2001 decision by a federal judge in Oregon, Michael Hogan, who ruled that the government could not lump hatchery and wild fish into the same group, or “evolutionarily significant unit,” for purposes of the Endangered Species Act while listing only the wild fish as protected.

Instead of appealing the decision or designating hatchery and wild fish as separate groups under the law, the National Marine Fisheries Service - over the objections of government scientists - decided in 2005 to take the numbers of hatchery fish into account when determining whether salmon runs are endangered or threatened. Coughenour said the agency's motives in declining to appeal Hogan's decision “strike the court as rather transparent,” implying they were based on political rather than scientific concerns.

Hogan's ruling resulted in coastal coho salmon in Oregon being removed from the list of threatened species. This spring, building industry, farm and property rights groups asked him to expand his decision by invalidating Endangered Species Act listings for all 16 protected populations of salmon in Washington, Idaho, Oregon and California.

Sonya Jones, a Washington state-based attorney with the Pacific Legal Foundation of Sacramento, Calif., said Coughenour's rulings were in direct conflict with Hogan's and that the issue is ripe to be taken up by the 9th U.S. Circuit Court of Appeals. Pacific Legal represents the property rights groups, including the Building Industry Association of Washington.

Coughenour noted his rulings could have the “happy result” of inviting appellate review.

The judges agree on two central points: that the government has the authority to list hatchery and wild salmon in the same population group, and that both hatchery and wild fish may be protected under the Endangered Species Act.

Where they disagree is that Hogan says the fisheries service must consider the hatchery and natural fish in a population group in determining whether the group deserves protection. Coughenour says the agency must consider the health of the natural stocks only.

“We haven't had a chance to analyze the rulings yet, other than to say the obvious, which is that we're disappointed,” said Brian Gorman, a spokesman for the fisheries service.

Kaitlin Lovell, salmon policy coordinator for Trout Unlimited, one of the conservation groups that challenged the policy, said the ruling could be especially significant if it persuades the fisheries service to start placing hatchery and wild fish in separate population groups, then protecting the wild stocks.

But she said further litigation is a more likely outcome.

“You can't look to hatcheries to make up the difference for wild fish any more,” she said. “This decision says you have to be looking at the health of the naturally spawning fish.”

The other organizations that sued include the National Wildlife Federation, the Pacific Coast Federation of Fishermens Associations and Oregon Wild.