VANCOUVER - A seafood company that prides itself on buying nothing but sustainable and legal fish says it has become a bycatch in an investigation into an alleged illegal First Nation salmon fishery.

Provincial court documents say the federal government is investigating the illegal catch of about 64,000 kilograms of prime sockeye salmon in the Johnstone Strait last August.

It's part of a wider investigation that a spokeswoman from the Department of Fisheries wouldn't elaborate on beyond saying no charges have yet been laid.

But the court documents show the Crown told the judge the investigation was extensive, involved more than one First Nation and concerned the various agreements between them and the federal government.

The documents show Pasco Seafood Enterprises Inc. purchased the fish last summer and began processing them. But Fisheries then seized 31 large totes of salmon saying it was illegally caught.

Pasco said in its statement it did everything by the book, checking the First Nations permit to fish and all other paper work authorizing the fishery.

"This case pertains to a dispute between the DFO and the First Nations band with regard to the interpretation of their fishing agreement," Pasco president Jason Ogilvie said in an email statement to The Canadian Press.

When the fish were being processed at the company's Richmond, B.C., plant, Fisheries officers inspected Pasco's paper and said it was complete and in order, Ogilvie said.

"But there was a question as to whether the First Nations band had the right to fish in the Johnstone Strait area."

An affidavit filed in provincial court by Fisheries officer Trevor Tomlin said the salmon were caught in a closed area and the fish harvesters didn't have a license to catch the fish.

The investigation came to light because Pasco asked the federal government to return seized documents and the $90,000 the government received from selling the salmon.

The government went to provincial court asking for a nine-month extension past the 90 days allowed to keep such evidence and proceeds.

In his ruling, Judge Dennis Schmidt extended the time for retention of the documents, but said he had no jurisdiction to extend the detention of the $90,000 proceeds being held by the Receiver General.

In the background of the judgment, Schmidt said the investigation involved an agreement signed last July between the federal government and some First Nations around an economic opportunity fishery.

His ruling said the unnamed First Nation conducted the fishery in the Johnstone Strait a month later and fisheries officers believe the salmon was caught illegally.

Kirsten Ruecker, communications advisor with the Department of Fisheries, could only say the issue remains under investigation. She wouldn't name the First Nations being investigated.

Ogilvie said Pasco's actions have not been called into question by DFO.

"In all circumstances, Pasco Seafood conducted its business wholly above board and acted with due diligence to ensure that all proper documents and permits required were in place for the purchases of this sockeye salmon from a First Nations economic opportunity fishery."

That fishery is different from food, social and ceremonial fishery B.C. First Nations rely on for their own use. The economic opportunity fishery allows First Nations to take part in a commercial fishery and sell the fish.

Todd Gerhart, a lawyer with the Public Prosecution Service of Canada, also wouldn't reveal details of the case, but confirmed it is appealing the judge's ruling over the order to return the $90,000.