There are warnings of a looming disaster in Macquarie Harbour on Tasmania's west coast, where the state's three leading producers intensively farm salmon next to a world heritage wilderness area.

Key points: Salmon producer says fish stocks in Macquarie Harbour need to be reduced

Salmon producer says fish stocks in Macquarie Harbour need to be reduced Last year 85,000 salmon suffocated in the harbour

Last year 85,000 salmon suffocated in the harbour February study showed fish were stressed, struggling breathe and had stopped feeding

Salmon farming is currently worth more than $700 million and the Tasmanian Government has committed to making it a $1 billion industry by 2030.

Tonight on Four Corners, Frances Bender, the co-founder of Tasmania's second largest salmon farming company Huon Aquaculture, has broken industry ranks to warn about what she says are the dangers of farming salmon in the state's pristine waters.

"My comments will be controversial because they'll be taken that I'm being critical of other players in the industry and I'm being critical of the Government," Ms Bender told Four Corners.

Frances Bender says the State Government has ignored the science. ( ABC News: Sophie Zoellner )

"But the simple fact of the matter is we can't help that. The facts speak for themselves. The science is speaking for itself. And there is no way that I can sit here and lie."

"This is not the politically correct thing to say and this is not the corporate thing to say, but it's me saying it and quite frankly we're just sick of it."

Government received confidential briefings on dangers

Born and raised in south-east Tasmania, Frances and Peter Bender began dabbling in salmon farming 30 years ago to bolster their sheep and cattle business.

The now ASX-listed company Huon Aquaculture this year posted revenue of more than $230 million and it employs 524 Tasmanians.

Do you know more about this story? Email mcdonald.alex@abc.net.au

Four Corners can reveal Huon Aquaculture has confidentially briefed the Tasmanian Government about the need to reduce fish stocks in Macquarie Harbour on three occasions this year.

The Government has also been provided with scientific reports and data showing concerning temperature spikes and dangerous drops in water oxygen levels in February this year.

The fish were recorded struggling to breathe and were so stressed they stopped feeding and went into survival mode.

Inside Tassal's hatchery where millions of baby salmon (pictured) are bred. ( ABC News: Four Corners )

Ms Bender said the science and Huon's pleas for change had been ignored by the State Government and the Department of Primary Industries, Parks, Water and Environment (DPIPWE).

"The Department can't claim ignorance," she said.

"It's concerning for my company, it's concerning for the region and everyone that lives there, it's concerning for the reputation of our industry.

"It's concerning for regional Tasmania and it's concerning for the brand that is Tasmania."

In May 2015 around 85,000 salmon belonging to the smallest of the big three producers, Petuna Seafoods, suffocated in Macquarie Harbour.

The storm surge pushed water that was lower in oxygen towards the surface of the harbour.

Petuna chief executive Mark Porter said salmon farming in Macquarie Harbour was having a "minimal" impact on the waterway.

Fish in the Macquarie Harbour have been recorded as having very high stress levels.

But Huon Aquaculture is now scaling back its operations in the harbour.

"The science is telling us that Macquarie Harbour is a harbour under stress," Ms Bender said.

Associate professor Tim Dempster from Melbourne University's sustainable aquaculture laboratory told Four Corners it was "ill-advised to have more fish in this harbour going through these conditions".

Instead of scaling back the number of fish being allowed in Macquarie Harbour, the secretary of the DPIPWE has increased the cap twice in the past two years.

Most recently, in April 2016 Tasmania's DPIPWE lifted the cap on the number of farmed salmon in Macquarie Harbour by 1,350 tonnes.

Dr Tim Dempster said the decision was "perplexing".

Industry divided over Macquarie Harbour

While Huon says Macquarie Harbour is under stress, the biggest salmon producer Tassal has a different view.

Tassal owns three leases in Macquarie Harbour and accounts for more than 40 per cent of the market, an ASX listed company with an annual revenue of $430 million.

Tassal director Mark Ryan says Macquarie Harbour is sustainable. ( ABC News )

Its chief executive Mark Ryan, a former chartered accountant with financial restructuring and turnaround firm KordaMentha, has told Four Corners Tassal's science shows Macquarie Harbour is a sustainable waterway.

"Different companies have different views on it," Mr Ryan said.

"Everyone wants a sustainable industry [in Macquarie Harbour] but people farm with different practices and that's okay."

Both the Tasmanian Minister for Primary Industries and the Premier declined to be interviewed by Four Corners.

In a statement, the State Government said a management framework was in place "to ensure the sustainable management of Macquarie Harbour into the future".

It said the Tasmanian Government liaised with salmon companies on a broad range of issues including environmental conditions.