The Marine Stewardship Council has launched an investigation after it emerged fish sold by Sainsbury's as MSC wild salmon was farmed.
The case has been referred by MSC chief executive Rupert Howes to the scheme's auditor, Accreditation Services International.
"While no system is infallible, the built-in checks and balances in the MSC system should catch any attempt at deliberate fraud," Howes said.
Sainsbury's branded the allegations "totally unfounded" after it was identified last week by an FSA survey into the mis-selling of fish. "We would never sell farmed fish as wild," said a spokeswoman. "Each batch of our Wild Alaskan Salmon is checked for traceability and chain of custody as soon as it arrives in this country. It is certified by the MSC, and the system is independently checked and audited."
The FSA survey found 15% of the 'wild' salmon sold in retailers came from farms. Harrods was also named in the survey, although the FSA did not allege foul play in either case.
Harrods also sought to play down the issue, saying it was probably a case of human error, because farmed and wild product were sold side by side.
Asda was caught selling farmed sea bass without telling shoppers and question marks hang over salmon bought at Tesco, Morrisons and Waitrose, as the FSA's scientific analysis was unable to establish whether the fish was wild or farmed.
Most cases where farmed fish was sold as wild occurred in independent fishmongers and affected sea bream and bass as well as salmon.
Fishmongers were caught providing the incorrect information about fish on sale in 75% of cases, the FSA said.
"It's not a question of misrepresentation, but of labelling," said a spokesman for the National Federation of Fishmongers. "To get all the information on to a label would require an A4-sized ticket, which ruins the display."