The supermarkets have adopted a wait-and-see approach as authorities work to save Tasmania's Maugean skate from extinction.
Salmon farming has contributed to a severe lack of dissolved oxygen in Macquarie Harbour - the only place on earth where the ancient skate still exists.
Current interventions include a captive breeding program to boost the remaining population of fewer than 1000 fish, and efforts to artificially pump oxygen into the harbour's depths.
Federal conservation advice for the skate had urged a reduction in farmed salmon loads before last summer, but that didn't happen.
On Friday, Coles and Woolworths told a greenwashing inquiry they were aware complaints had been made to the consumer watchdog about their Tasmanian salmon products.
Groups including Neighbours of Fish Farming have complained the supermarkets' own-brand salmon carry unqualified claims like "responsibly sourced" with the potential to mislead consumers about the environmental harms of Tasmanian salmon.
Authorities are working to save the Maugean skate, whose only habitat is Macquarie Harbour. (HANDOUT/JANE RUCKERT)
The complaint also alleges the supermarkets are omitting significant information about the extinction risk salmon farming poses to the skate.
NOFF campaigner Jessica Coughlan told Friday's hearing there were a range of certification standards for Tasmanian salmon.
But two - the Aquaculture Stewardship Council and the RSPCA - no longer certify salmon from Macquarie Harbour on environmental grounds.
She said the retailers had "shopped around" for others that would certify salmon farmed in the harbour, allowing them to continue to make claims about responsible sourcing.
Duncan Leadbitter from the Aquaculture Stewardship Council told senators there were no longer any ASC-certified salmon farms in Macquarie Harbour.
He said salmon producers Tassal and Petuna used to hold ASC certificates in Macquarie Harbour but the companies walked away from them.
"They were withdrawn because they were starting to breach the dissolved oxygen requirements of our salmon standard - excessively," Mr Leadbitter said.
"And so they withdraw the certifications that they had for their farms in Macquarie Harbour."
ASC still certifies salmon from other Tasmanian locations.
Greens senator Sarah Hanson-Young asked why Coles and Woolworths did not display the logos of the independent certification schemes they use on the packets of their own-brand Tasmanian salmon.
Salmon farming has contributed to a severe lack of dissolved oxygen in Macquarie Harbour. (AP PHOTO)
She said they instead used their own logos declaring the products to be "responsibly sourced" but it was entirely unclear to consumers who'd verified that.
Woolworths' chief sustainability officer Rachel Elliott said its "responsibly sourced" logo was about giving consumers an overview "around the due diligence approach that we have undertaken with respect to seafood".
"This particular claim does reflect careful due diligence in respect to our seafood is third-party certified, through approved certification bodies."
She said links were provided on the back of packs to help customers understand what the logo means, and that third-party certification schemes are involved.
Brooke Donnelly, the general manager for sustainability at Coles, said its own-brand salmon products must be certified to the standards set by is certification partners, which include ASC.
But she said the issue was complex and evolving.
"Those standards and certifications that are fit for purpose at this particular point in time will need to evolve over time."
She said Coles had reviewed its own-brand salmon sourcing strategy.
"The intention ... is to better understand what the near, medium and long-term options to diversity our salmon sourcing approach is, and explore future opportunities."
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