On Friday, representatives from RSPCA Assured, the Animal and Plant Health Agency and Marine Scotland visited the Scottish Sea Farms site at Loch Spelve near Dalnaha.
It follows the release by Scottish Salmon Watch (SSW) of covertly-filmed footage and still images which showed wounds on live fish and what it calls fin damage.
SSW lodged a formal complaint alleging breaches of the Animal Health and Welfare (Scotland) Act 2006 and contacted the three organisations, along with Police Scotland’s Wildlife Crime Unit.
But Scottish Sea Farms say the wounds were caused by seal attacks and have rejected subsequent footage this week as 'inaccurate and unfair'.
It has resulted in the site having its RSPCA accreditation temporarily suspended while the matter is investigated.
Scottish Sea Farms added the visits to the site on Friday are 'due process' when a complaint is made.
Of the visits, it said: 'These same representatives will now separately prepare their reports. Whilst it's not our place to speak on their behalf, what we can say is our statement still stands: the original footage clearly depicts the harm that natural predators such as seals can cause.'
The complaint by Scottish Salmon Watch stated: '[Video footage clearly shows fin damage, skin lesions, open wounds (which may be winter ulcer), mouth rot, lice infestation and indicates welfare and disease problems.'
Don Staniford, director of Scottish Salmon Watch, said: 'Rest assured that RSPCA accreditation of Scottish salmon as ‘welfare-friendly’ is a sham, scam and consumer con. Video evidence shot last week and last year at RSPCA Assured salmon farms across Scotland exposes endemic welfare abuse, disease problems and mass mortalities.'
Scottish Sea Farms denied the injuries are the result of untreated disease or parasites.
In a statement, the company's head of fish health and welfare Dr Ralph Bickerdike said: 'Contrary to the claims being made, the footage clearly depicts the damage that seals can cause to fish, in much the same way that foxes can harm or kill chickens or lambs for example.
'Our farm teams are vigilant to presence of any damage caused to our salmon, removing affected fish as swiftly as possible and ensuring they are dispatched quickly and humanely in the interest of high animal welfare.'
The Loch Spelve site supplies M&S with Lochmuir brand salmon and is subject to inspections by RSPCA Assured, a not-for-profit arm of animal welfare body RSPCA.
A spokesperson for RSPCA Assured said: 'We are very concerned by some of this footage and have suspended the farm whilst we urgently investigate.'
A Scottish Government spokesperson said the Animal and Plant Health Agency (APHA) would investigate.
'A member of the Fish Health Inspectorate will be in attendance at a site visit to examine the fish health aspects of the case,' it said.
'Our 10-year Farmed Fish Health Framework aims to significantly improve the health of farmed fish in Scotland and should lead to a significant reduction in mortality.
'The Framework commits industry, government, vets, trade associations and Scotland’s Aquaculture Innovation Centre to work together to provide a strategic, evidence-based approach to the short and long-term improvement of fish health in Scotland.'
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