Salmon companies have responded to the revelation that more than a million farmed fish died within six months in Macquarie Harbour.

Tasmania's Environment Protection Authority (EPA) has confirmed 1.35 million salmon died in Macquarie Harbour since last October.

The EPA will reduce Macquarie Harbour's biomass limit by 21 per cent over the next two years.

The deaths were linked primarily to an outbreak of pilchard orthomyxovirus (POMV), transferred from wild populations.

EPA director Wes Ford says the “mixing of young fish with old fish” in 2017 could exacerbate the likelihood of disease in the population.

“POMV can be exacerbated by stress caused by heat, low oxygen, and I think this summer we've seen some elevated temperatures and clearly some concerns about oxygen.”

The companies affected by the mass fish kill have now issued statements.

Huon Aquaculture says it warned other farmers and the Government last year that mixing young and old fish creates new risks.

“Since then, we understand the practice [of mixing age groups] will cease in the future. Huon does not mix year classes of fish,” the company said.

Tassal issued a statement saying the fish deaths did not impact its activities.

“The POMV situation stabilised quickly and these fish were replaced quickly from our nursery, given they were only juvenile,” it said.

“Tassal and Petuna have worked proactively to embed better biosecurity and environmental outcomes for the harbour via a joint-venture farming operation, which enables both separation of year, class and extended fallowing periods for leases.”

Salmon farmer Petuna said it culled two fish pen populations to help reduce the spread of the disease on its leases.

It has not disclosed its individual stock losses for the summer.

“Under the [Area Management] Agreement, each company confidentially provides its own specific data, which is then independently collated to ensure each company's competitive market positions are not compromised,” Petuna said in a statement.

“The company is not required to report this information other than to the Marine Farming Branch, which it does monthly.”

Environment Tasmania says over 2,000 Tasmanians have petitioned salmon companies to release their fish death tolls.

The Greens have called on the Government to step in and impose a moratorium on all fish farming.