The Australian government Tuesday sought to change its environmental protection laws to prevent a controversial super-trawler from fishing in its waters amid concerns about the by-catch.

The Dutch-owned 9,500-tonne FV Margiris, recently reflagged as the Abel Tasman, is currently docked at Port Lincoln in South Australia and was preparing to set sail.

But under new laws it would not be able to fish until new scientific research into the environmental impact had been carried out, which could take up to two years.

Environment Minister Tony Burke earlier sought legal advice about whether he could intervene over concerns that dolphins, seals, seabirds and other marine life would inadvertently get swept up in the ship's huge nets.

However, he was limited by the current legislation, prompting centre-left Labor to announce it would introduce new laws later Tuesday that, if passed, would extend Burke's powers.

"If we get this wrong there are risks to the environment, to commercial operators and to everyone who loves fishing and they are risks I am not prepared to take," Burke said.

"There has never been a fishing vessel of this capacity in Australia before and the Environment Protection and Biodiversity Conservation Act needs to be updated so that it can deal with it."

The amendment would prohibit the 143-metre (469-foot) trawler from fishing in Australian waters until the further assessment was undertaken by an expert panel.

There were protests among conservation groups and local fishermen when it was announced earlier this year that the ship would fish off Tasmania, and Greenpeace protesters tried to prevent it docking in Port Lincoln.

Greenpeace welcomed Tuesday's decision as sending a message "to the global super-sized fishing fleets that world community opposition is growing to their unsustainable business model".

"The global overfishing problem has not gone away," added Greenpeace head of campaigns Ben Pearson.

"There is 2.5 times more fishing capacity in the world than there are fish.

"This decision will put pressure on the European Union to withdraw their subsidies from the super trawler fleet and is a step towards more sustainable fishing."

The Australian Fisheries Management Authority has dismissed concerns about over-fishing, saying the trawler would be allowed to catch just 10 percent of available fish and would have little, if any, impact on the broader eco-system.

The trawler's Australian operator, Seafish Tasmania, told the Sydney Morning Herald it may take legal action against the government, but "we haven't got that far yet".