The rules published in the Canada Gazette this week allow some pesticides to be used provided they receive federal approval and follow rules enforced by the federal Fisheries Department.
A federal spokesman says the rules clarify the use of pesticides, a grey area in the past because under the federal Fisheries Act dumping "deleterious substances" in the ocean was illegal.
Some fish farms use pesticides on their pens to rid Atlantic salmon of sea lice.
Eric Gilbert, director general of aquaculture management, says the changes to the Aquaculture Activities Regulations require companies to report any deaths of marine life near their pens.
He said officers are being trained to investigate if pesticides are the cause and to review applications by the companies to use the chemicals.
"If they (company employees) see one dead fish around the facility ... they have to immediately call a fishery officer. ... In the past we didn't have that," said Gilbert in a telephone interview.
Maria Recchia, director of the Fundy North Fishermen's Association, says she's concerned there is too much discretion on the part of the industry to report problems resulting from pesticide use.
She said an industry where a large operator was fined $500,000 in 2013 for using an unapproved pesticide needs more direct oversight.
"You have an industry that went through a big court case on illegal use of pesticides and you put in regulations that ... in our opinion reduce the amount of monitoring government agencies are doing," said Recchia in a telephone interview.
Gilbert says there are significant fines if the industry doesn't report as required under the law.
Recchia also said in the past Environment Canada played a role in studying the impact of pesticides on marine life and in overseeing their use, and she's concerned the agency will play a reduced role under the regulations.
Rob Johnson, a spokesman on the issue for the Ecology Action Centre in Halifax, says he's concerned the pesticide approval process through the Pest Management Regulatory Agency will be guided by Health Canada.
"That agency has a health mandate but little expertise in environmental protection," he said.
The Atlantic Canada Fish Farmers Association said in a news release earlier this week the rules simplify a complex and overlapping regulatory system and will help the growth of the salmon farming industry.
"Only treatments that have undergone extensive risk assessments by Health Canada to ensure they are safe for salmon and other species, the environment and human health are registered for use," says the release.
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