Two international aquaculture companies are heading to court to try to quash a recent federal decision to phase out controversial fish farms in the Discovery Islands.

Mowi Canada West and Cermaq Canada want the Federal Court of Canada to set aside federal Fisheries Minister Bernadette Jordan's decision - in whole or in part - to phase out salmon farming operations in the region by the end of June 2022.

But First Nations supporting Jordan's decision say any reversals of the plan by the court would come at the cost of the inherent rights of Indigenous people.

The two fish farm companies are seeking costs and an injunction to suspend the decision, or parts of it, from going ahead until the court hears their applications

On Dec. 17, Jordan announced licences for 19 operations in the waters near Campbell River on Vancouver Island were being renewed for the last time and no new fish could be transferred to the salmon farms during the 18-month period.

The fisheries minister said her decision was largely the result of overwhelming opposition to the farms expressed by the region's seven First Nations during government-to-government consultations.

Mowi and Cermaq stated in the court application that the fisheries minister gave no advance warning of the decision, and did not allow the companies to provide input on its negative impacts.

The minister's announcement followed heated public debate around the fate of the fish farms and the risks they might pose to wild salmon stocks.

The farms are on key migration routes for wild juvenile salmon, and eliminating operations in the Discovery Islands was a recommendation made by the 2012 Cohen Commission investigating the decline of Fraser River sockeye.

However, the recommendation depended on Fisheries and Oceans Canada (DFO) finding the fish farms posed a danger to wild sockeye.

At the end of September, DFO concluded the farm operations posed minimal risk to Fraser River sockeye after studying nine different fish farm diseases.

Both Mowi and Cermaq argue in their applications that Jordan's decision was unlawful, unreasonable or procedurally unfair.

Cermaq said DFO's decision not to allow any new fish into its three Discovery Islands farms will force the cull of millions of juvenile fish scheduled for transfer to the region, the loss of 20 per cent of its production volume, and the potential closure of a hatchery.

The company also said 21 direct jobs are endangered, in addition to others employed in supporting positions, with total annual wages in the millions of dollars.

Mowi stated their affected farms represent 30 per cent of the company's operations and 645 direct jobs, many held by First Nation employees.

The largest operator in the region, Mowi owns 13 of the salmon farms impacted - nine of which were empty of fish when the decision was announced, according to DFO.

Both companies said the millions of fish slated for transfer take approximately five years to rear - starting with the selection of brood stock, the spawning of fish, hatching eggs, and finally raising fish until the smolts are ready to grow out in ocean pens.

DFO departed from past practice in failing to provide advance warning before making decisions that will materially affect, severely impair and end operations without providing operators a chance to provide input into the decision, the companies said.

Jordan also relied solely on input from her consultations with area First Nations, and failed to take social, economic and scientific considerations into account, the companies said.

Bob Chamberlin, a former vice-president of the Union of B.C. Indian Chiefs and a longtime advocate for wild salmon, said he wasn't surprised to hear the aquaculture companies want to challenge DFO's decision.

Jordan's announcement was the result of consulting with the Homalco, Klahoose, K'omoks, Kwiakah, Tla'amin, We Wai Kai and Wei Wai Kum First Nations about whether to renew licences for the fish farms operating in their traditional territories, he said.

But more than 100 First Nations dependent on wild salmon elsewhere on the coast and along the Fraser River also support the removal of the salmon farms, Chamberlin said.

Aquaculture companies regularly express concern about how closing the region's fish farms will negatively affect First Nations employees, communities, and partners, Chamberlin said.

Yet the same companies are willing to challenge a decision by the ministry that is respectful of the inherent Indigenous rights of First Nations, both within the region and across the province.

“They only respect us until they disagree with something,” Chamberlin said. “So, really, it's a conditional acceptance of our human rights.”

Homalco Chief Darren Blaney said DFO has had conflicting roles as both a promoter of fish farms and a regulator tasked with protecting wild salmon.

Aquaculture companies haven't faced many decisions contrary to their interests before DFO's recent decision, he said.

“They've gotten comfortable, and they didn't bother to address the issues they were creating with sea lice and diseases,” Blaney said.

“They never looked into closed containment or fish farming on land because they've had a (free ride) in the ocean.”

Sumas First Nation Chief Dalton Silver said the phasing out of the fish farms might impact jobs and revenue, but protecting depleted wild salmon is a question of food security for Indigenous people.

“Those who are benefiting from the fish farms are few, (and) at a great expense to the environment and to wild salmon, and many First Nations,” said Silver, who is also fisheries representative for the Union of B.C. Indian Chiefs.

The two aquaculture companies may be frustrated by a lack of consultation, but that's a situation First Nations have a lot of experience with, Silver observed.

“The non-consultation argument is something we've had for a long, long time,” Silver said. “No one talked to us about certain things that had great effect on our way of life, and are still affecting us.”

Chamberlin said he had trouble believing aquaculture companies were entirely surprised by Jordan's decision, given the Cohen Commission recommended the closure of the farms in December 2020 if DFO determined they posed a minimal risk to wild salmon.

Plus, the fisheries minister is developing a plan that is due in 2025 to transition away from open-net pen salmon farms in B.C. waters, Chamberlin added.

“The writing was certainly on the wall. It seems to me, (the companies) weren't proactive,” Chamberlin said.

“Their lack of business planning shouldn't be a legal starting point to overturn a decision made in consultation with First Nations.”

First Nations rights will be the collateral damage if the court decides in favour of the agriculture industry, Chamberlin added.

“This could result in a message that Crown process with a company is more important, or trumps respect for Aboriginal rights - whether that is the intention or not,” he said.

Jordan's office said Wednesday the minister is aware certain companies have asked for a judicial review of her decision regarding aquaculture licences in the Discovery Islands.

“As the matter is now before the courts, it would be inappropriate to comment at this time,”the ministry said.