The fish farming company claimed the government and the EPA had failed to effectively regulate salmon farming activity in Macquarie Harbour.

Huon Aquaculture alleged that too high a biomass cap had been set in the harbour – which, in this case, means the amount of salmon in a given area – after the EPA set the cap at 14,000 tonnes in January.

The company’s executive director Frances Bender said she was “pleading” with EPA director Wes Ford to release IMAS’ findings to the public.

“I don’t see how you can interpret no oxygen at the bottom of the harbour and the fauna in the sediments being deceased, as being anything [else],” Mrs Bender said.

Mr Ford said that given the nature of the legal proceedings, he would be unable to comment at this time.

Mrs Bender, meanwhile, said the government seemed to be “completely ignoring” IMAS’ science.

Her company recommended a biomass cap of fewer than 10,000 tonnes.

The lack of oxygen in the water at Macquarie Harbour is said to be caused by a high volume of fish and the sediment it sends to the harbour floor.

Huon Aquaculture is one of three marine farming companies with a presence at Macquarie Harbour: the others being Tassal and Petuna Seafoods.

Primary Industries Minister Jeremy Rockliff said there was “no greater supporter” of Tasmania’s salmon industry than the state government.

He said the industry was “among the best regulated in the world”.

But Greens environment spokesperson Rosalie Woodruff was of another mind.

“As the government won’t listen to impartial scientific evidence … about the need to regulate for the future, they'll now be forced to explain themselves in a court of law,” Ms Woodruff said.

The expansion of marine farming in Macquarie Harbour was overseen in 2012 by then federal Environment Minister Tony Burke.

Huon Aquaculture believed the conditions imposed by Mr Burke’s decision were not being abided by, which was why proceedings had been filed to the Federal Court.

There has been salmon farming in Macquarie Harbour since the early 1990s.