Anti-fish farm campaigner, Don Staniford, a director of SSW, said the photographs and videos were secretly filmed at four Mowi-run farms across Argyll and Bute - two in Shuna Sound and two in the Sound of Jura - over the weekend of July 16-17.
However, in a robust response running to more than 500 words, Mowi suggested they were 'isolated examples' and were not 'representative' of the health of fish raised at its farms.
But Mr Staniford, with support from Scottish charity Animal Concern and Friends of Loch Creran, said the footage showed fish with serious eye, head, snout and fin damage.
Mowi said 'tracking and tending' to injured fish was difficult due to the size of the pens as the fish tended to flee when attempts were made to remove them.
Mr Staniford has lodged a complaint with the Animal and Plant Health Agency, the Scottish Government and Police Scotland’s wildlife crime unit.
He called for the farms' RSPCA Assured certification to be rescinded 'immediately'.
RSPCA Assured said: 'We are concerned by some of the images that have been shared with us. As soon as they were brought to our attention, we immediately launched an investigation into those farms we understand are featured. These investigations are ongoing.
'Animal welfare is our absolute priority and the focus of our assurance scheme, therefore any complaints are always taken very seriously and thoroughly looked into as standard practice.'
Police Scotland have also been contacted for comment.
Mowi said 'similar allegations' were filed in March and also triggered an investigation by the RSCPA along with physical inspections by RSPCA Assured auditors, with 'no evidence' found to support the claims made.
Mowi said: 'As is the case with all types of farming, there will unfortunately be times when individual animals are in distress, and these isolated examples can be understandably concerning to the public as well as the farmer.
'Farmers and veterinarians will do whatever they can to treat animals under their care, or, when circumstances require it, may have to choose to humanely euthanise the animal.'
Ben Hadfield, chief operating officer of Mowi Scotland, added: 'We care very much for the welfare of our salmon, every day and don’t like to see even one animal suffer.
'Our experienced farmers are supported by fish health experts and veterinarians that help to ensure animal welfare is attended to every day, and these results are inspected by professional third-party organisations.'
Mowi also released an image of a fish it said was taken from one of its farms on the same date.
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But John Robins of the charity Animal Concern, said in the Scottish Salmon Watch press release that the group had obtained evidence of 'severe suffering'.
Mr Robins said: 'Since the welfare of farmed fish was recognised in the Animal Health and Welfare (Scotland) Act 2006 I have been trying unsuccessfully to have that legislation used to stop this suffering.'
And Maggie Brotherston of Friends of Loch Creran said 'secret filming' was vital to exposing welfare on salmon farms and praised the 'remarkable job of ground-truthing'.
Mr Staniford, called on the Scottish Government to 'immediately close down' the farms and for supermarkets to stop selling RSPCA Assured Scottish salmon.
Supermarket company Sainsbury's said: 'All our suppliers have to meet our high welfare standards and are regularly required to demonstrate this.
'This includes site visits and regular health and data reviews to make sure they also comply with all rules and regulations.'
It said it had been in touch with Mowi and the company had shared the 'full context' of the images and footage.
A Scottish Government spokesperson said it received allegations of alleged breaches of the Animal Health and Welfare (Scotland) Act 2006.
'The Scottish Government takes fish health and welfare seriously and the complaint has been discussed with the Animal Plant Health Agency (APHA) who are responsible for investigating allegations of poor animal welfare on farms.
'The complaint has also been considered as a matter of urgency by officials within Marine Scotland’s Fish Health Inspectorate (FHI) who have contacted the company to discuss the sites in question and investigate from a mortality, sea lice and disease perspective.
'These investigations by FHI, which include considering sea lice information collected weekly from all sites, have concluded that there are no obvious sea lice or mortality issues at a population level at any of the sites involved in the allegation and that appropriate measures are in place to control sea lice, remove mortalities and ensure adequate fish health management at the sites in question. The FHI are not responsible for investigating welfare complaints.'
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