Officials with Snow Island Salmon say a decision by the province to reject an application for a fish farm operation along the Eastern Shore has wide implications and jeopardizes the future of the company in Nova Scotia.

"Yesterday's surprise announcement has shaken our confidence, whether we have a future in Nova Scotia. What we need right now is for the Nova Scotia government to demonstrate through action that it's prepared to allow small- and medium-sized companies like ourselves to operate in this province," said Shane Borthwick, the vice-president of operations at Snow Island Salmon.

"Today, all members of the Aquaculture Association of Nova Scotia have not had support. So the question is, is there a future for aquaculture in this province?"

Snow Island Salmon Inc. — the Canadian subsidiary of Scottish aquaculture company Loch Duart Ltd. — wanted to operate a salmon farm at Shoal Bay near Sheet Harbour.

The application went through a 22-month review by Nova Scotia Fisheries and Aquaculture as well as Fisheries and Oceans Canada. Ultimately, the federal department decided the proposed Shoal Bay site posed a "low risk to fish habitat" but a "moderate risk to wild Atlantic salmon."

"We addressed any and all of the concerns that were raised to us and I think what's most troubling is the length of time and delay in this particular review and then such a prompt decision without even discussion related to the provincial concerns on this," Borthwick said Thursday.

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A Scotland-based company's application to develop salmon fish farms on Nova Scotia's Eastern Shore has been rejected. (CBC)

"The fact is all of the rivers in close proximity to the Shoal Bay application don't have Atlantic salmon. That was in the Department of Fisheries and Oceans report, so it seems to be inconsistent."

Sterling Belliveau, the provincial Minister of Fisheries and Aquaculture, said the decision was based on science and said it's not a sign that the government is changing its support for fish farms, which was part of its aquaculture strategy released last year.

Borthwick said his farms have never had any fish escapes and he doesn't understand the province's concerns because the Eastern Shore location is 20 kilometres from any river with an active wild salmon run.

"At this point in time, we need to better understand the concerns of the province and I think that's one of the concerns we have. We've spent 22 months, over $8 million, we've been invited to the province, we put a world-class farming model on the table that has never been done before," he said.

"This model has been recognized for its sustainability practices and quite honestly, these fish under this type of model has been good enough for the royal family but it doesn't seem to be good enough for the province of Nova Scotia."

Snow Island Salmon also has an application for a fish farm in Spry Harbour. No decision has been made on that proposal.

The company had previously applied for another fish farm in Beaver Harbour but it withdrew that application late last year because of its proximity to wild salmon populations.

"We have self-imposed many restrictions related to stocking densities, distance between farms, away from rivers, reached out to conservation groups, the science community, we've done more than anyone has ever done. This isn't acceptable," said Borthwick.

"I question the decision of the province, whether they fully have an appreciation for the impact that this may have."