The bacterial infection at the North Shore site is believed to be pasteurella skyensis, a salmon bacteria first identified around 2002 and linked with Skye. It is being treated with antibiotics.
Marine Harvest spokesman Steve Bracken said: "We are trying to treat the fish with antibiotic and they seem to be taking that. Hopefully we will see the effect of that."
He said the fish were around 3kg, adding: "Some of the fish are absolutely fine, but then you've got these others that have succumbed to this pasteurella skyensis. Some fish will be affected more than others, and that's the same with any animal infection.
"Those that are still reasonably fit and healthy and will take the antibiotic, that's a good sign. But there will be a mortality and it will continue."
Bracken was unable to put a figure on losses at this stage. He said: "We've just got to work our way through it and at the end we'll know what we've got."
Marine Harvest has one other stocked site on the loch, at Tabhaigh, to the east of North Shore, and Bracken said the company was ensuring strict biosecurity to make sure it didn't accidentally transfer the infection. He said that while there was the possibility of the bacteria being carried to the other site in the water, "what we don't want is to create that situation ourselves".
The company has two sites at North Shore but is treating the area as one farm in terms of tackling the skyensis outbreak. According to Marine Scotland figures, North Shore West held 1,505 tonnes of fish in June, while North Shore East held 1,062 tonnes.