Fish-farming opponents from B.C. and the United States wrote the Commission for Environmental Co-operation in October 2012, alleging the federal government wasn't enforcing the Fisheries Act.
The groups claim Ottawa is exposing wild salmon to sea lice, disease, toxic chemicals and concentrated waste.
Environment Canada wrote the commission last month, arguing a continuation of the complaint would interfere with two legal cases that are currently underway.
The commission has now written back asking for further explanation within 30 working days and has a set final deadline of Dec. 17.
According to their submission, the complainants want the commission to write what's known as a factual record on the issue.
"The submitters may be able to use that to press the government to make changes in the way they enforce the law," said Hugh Benevides, legal officer for the commission in Montreal.
Chief Bob Chamberlin of the Kwikwasu'tinuxw Haxwa'mis First Nation in Alert Bay, B.C., said a factual record would also put the issue on the record.
"The NAFTA agreement ... has some teeth, some validity between the governments, and it's important for us because what we're doing is we want to raise the awareness about what we see the impact at an international level, and that's what the NAFTA agreement provides us," said Chamberlin.
He said the majority of product that comes out of his territory goes to the United States.
Also listed as complainants are Jeff Miller of the Center for Biological Diversity in San Francisco, Calif.; Alexandra Morton of the Pacific Coast Wild Salmon Society in Sointula, B.C.; Zeke Grader of the Pacific Coast Federation of Fishermen's Associations in San Francisco; and Prof. Michael Harris and clinical fellow Kevin Lynch of the Environmental Law Clinic at the University of Denver Sturm College of Law.
Specifically, the complainants argue the federal government isn't enforcing two sections of the Fisheries Act.
Section 35, they argue, prohibits any work or undertaking that results in harmful alteration or disruption to fish habitat without valid authorization. The complaint involves more than 100 commercial salmon farms operating on B.C.'s coast.
They also point to Section 36, which prohibits the deposit of deleterious substances in water frequented by fish unless a deposit is authorized by regulation. The groups' complaint refers to a neurotoxic chemical known as emamectin benzoate that's used to treat sea lice.
"The potential for British Columbia salmon feedlots to introduce, amplify and spread pathogens also jeopardizes the health of every other wild salmon run along the Pacific Coast, as well as the entire West Coast salmon fishing industry, because these stocks co-mingle," says the submission.
Environment Canada could not be reached for comment, but in an Oct. 4 letter, the agency refers to separate lawsuit launched by Morton and Chamberlin's First Nation.
"The government of Canada is concerned that proceeding with the B.C. Salmon Farms submission would result in the duplication and/or interference with these domestic legal actions," wrote Dan McDougall, assistant deputy minister.
He also referred to Canada's commitment under Article 6 of the NAFTA agreement to ensure people with legally recognized interests are given appropriate access to legal proceedings, and that requests for investigations receive due consideration under Canadian law.
McDougall asks the commission to terminate the proceedings.
Meantime, Mary Ellen Walling, executive director of the B.C. Salmon Farmers Association, said in a statement her members are confident they are raising fish in a responsible way.
"We believe our farmers are reducing the risk on wild salmon by providing an alternate source to this popular food choice," she said in an email, adding the submission repeats many pieces of misinformation that have been corrected by experts and extensive research.
"We are confident that will be made clear as the process unfolds."
The North American Agreement on Environmental Co-operation was signed by the governments of Canada, Mexico and the U.S. in 1993.
The commission that oversees the agreement is tasked with supporting the governments' efforts to green North America's economy, promote a low-carbon economy, address climate change and protect the continent's environment, as well as the health of citizens.
Like this article? Follow our Facebook pageOr follow us on TwitterFollow @HuffPostBC
Also on HuffPost