Cooke Aquaculture says the license termination by the state Department of Natural Resources results from a “misunderstanding,” but the state says the decision is final.

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Cooke Aquaculture says its troubles with state regulators that led to the shutdown of its Port Angeles Atlantic salmon farm last week are all a misunderstanding, but the decision to revoke Cooke’s license is final.

“An inspection of the Port Angeles site from December 4-9 revealed significant lease violations that endanger public safety and the health of Puget Sound,” Carlo Davis, communications director for the state Department of Natural Resources (DNR), wrote in an email to The Seattle Times on Monday.

“The decision by Commissioner of Public Lands Hilary Franz to terminate the lease is final. DNR will work cooperatively with Cooke Aquaculture Pacific to dismantle the facility in a safe and appropriate manner.”

There are nearly 700,000 Atlantic salmon in the pens at the farm, which first went into operation in 1984. It has had a series of owners, most recently Cooke, which bought it from Icicle Seafoods.

Franz terminated Cooke’s lease Friday, stating during inspections the week of Dec. 4 the farm was found to be outside of its lease boundaries. Anchor lines were also damaged or missing, and Styrofoam used to float portions of the farm was not encapsulated as required.

Cooke Aquaculture issued a news release Sunday in which Joel Richardson, vice president of public relations for Cook, stated the termination was a surprise and “likely the result of miscommunication with DNR.”

Before receipt of the Dec. 15 termination notice, Cooke Aquaculture Pacific had already addressed and completed — or was addressing — each of the inspection items cited by DNR as the basis for its decision to terminate the Port Angeles lease, Richardson wrote.

“We do not believe DNR understood that we were aware of and in the process of addressing these items and we do not believe the facts support DNR’s decision to terminate the lease.”

Richardson added, “We look forward to discussing the notice of default with DNR officials to ensure that they are fully aware of all the work completed prior to their notice, as well as the enhancements we have scheduled. DNR has acted punitively without fully understanding the facts or reaching out to us for constructive dialogue.”

Others were delighted by Franz’s action, saying that it was about time, and that they hope for a shutdown of all of Cooke’s other seven farms around Puget Sound.

“I want them all gone. They can absorb the loss and never come back,” Tom Wooten, chairman of the Samish Indian Nation, said of Cooke, one of the world’s largest farmers of Atlantic salmon, with operations in several countries.

Another of Cooke’s Washington farms, at Cypress Island, collapsed last summer, allowing the escape of about 160,000 Atlantic salmon into Puget Sound.

About 105,000 Atlantics are still unaccounted for in Puget Sound — and are still turning up in local rivers. The Upper Skagit Tribe most recently caught Atlantics 53 miles up river on the Skagit, during a fishery for chum for the tribe’s hatchery, said Scott Schuyler, natural-resources director for the tribe. That was even farther up river than on a previous fishing trip this month, 43 miles up river.

“We have canceled our chum fishery; we can’t catch any chum, but we keep catching Atlantics,” Schuyler said Monday. Cooke had doubted the tribe’s report, with company spokeswoman Nell Halse stating the company would do its own investigation of the ongoing catches.

However, the fish have already been confirmed to be Cooke’s by the Washington Department of Fish and Wildlife, by examination of ear bones in the fish, marked in the hatchery by Cooke.

Several state lawmakers have advanced bills in the Legislature to shut down Atlantic salmon net-pen farming in Puget Sound, including emergency legislation by two GOP lawmakers to close it down immediately upon the governor’s signature.

Washington state tribes with treaty rights to fish for salmon in Puget Sound have also called for termination of Atlantic salmon net-pen farming in Puget Sound.

Atlantic salmon farming in open-water net pens is banned in California and Alaska and not practiced in Oregon. Washington is the only West Coast state that now is home to Atlantic salmon farms in public waters. The Department of Natural Resources holds all Cooke’s salmon-farm leases.

Franz initiated inspections of all of Cooke’s farms after the salmon escape in August. Those inspections are ongoing. An investigation by multiple state agencies into the salmon escape also is underway.