MARINE science has been ''trashed'' by Environment Minister Tony Burke's decision to ban the super-trawler Abel Tasman, says the body representing Australian fishing businesses.

A public uprising against the presence of controversial super trawler the Abel Tasman has prompted the Federal Government to introduce new laws to ban it from Australian waters for at least two years.

Environment Minister Tony Burke will introduce new laws to parliament today to give the government more powers to stop the trawler and protect Australian fisheries.

Existing environmental laws do not legislate for vessels of the Abel Tasman's size and haul potential.

Chairman of the Commonwealth Fisheries Association (CFA) Martin Exel says Australia's reputation as one of the world's best fisheries managers has been forgotten in the government's rush to stop the trawler.

''The trashing of the science, and I think that was particularly evident in Mr Burke's statement, was very, very disappointing,'' Mr Exel told Australian Associated Press today.

''The science in Australia is world-leading. The scientists on the small pelagic fishery ... have international awards for their marine science expertise and skills.''

Mr Exel said the last-gasp decision to amend legislation and ban the 142-metre factory ship was disappointing.

''It's outside of the current legislative provisions so it is a retrospective action for the company and that is worrying,'' he said.

''But I am sure that they would adequately compensate the company.''

media_camera Super trawler graphic

Mr Exel, though, admitted government and organisations like his own needed to make a better public case for the science behind decisions and welcomed the announced review of the Australian Fisheries Management Act.

The vessel is licensed to take 18,000 tonnes of mainly mackerel and red bait fish, using 600-metre nets.

Public sentiment against the super trawler and intense lobbying from environmental groups prompted action, Mr Burke admitted.

''There has been a massive public focus on this, the key relevance of that has been the extent to which it has undermined confidence in our management,'' Mr Burke said.

''There is no doubt that confidence in our management of fisheries and bycatch issues has been undermined.''

Mr Burke said concern over the trawler's ability to catch a huge amount of fish, and kill many protected animals in a localised area, also prompted the law change.

He said the Environment Protection and Biodiversity Conservation Act will be updated.

''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,'' he said.

''There has never been a fishing vessel of this capacity in Australia before and the EPBC Act needs to be updated so that it can deal with it.''

media_camera The Abel Tasman trawler is currently docked in Port Lincoln. Picture: Ivon Perrin

The minister said he had explored all options under the Environment Protection and Biodiversity Conservation Act to limit the impact of the super trawler.

''But I want to do more,'' he said.

Mr Burke said the proposed legislation would stop the super trawler from fishing in Commonwealth waters while a further assessment was undertaken by an expert panel.

''If the amendment I am proposing is passed by the parliament, I will be able to work with the fisheries minister to set up an expert panel to conduct an assessment of all of the potential impacts of the Abel Tasman before it can be given approval to fish in Commonwealth waters,'' he said.

The proposed amendment would stop the super trawler, or similar vessels, fishing in Australian waters for up to two years.

This would allow time to conduct scientific work and assess expert advice, Mr Burke said.

''While that work is being undertaken the relevant fishing activity cannot take place within Australian waters for a period of up to two years,'' he said.

''This creates a situation where we are not flying blind.''

Mr Burke said it would give the government the information it wanted to guarantee sustainability.

Mr Burke and Fisheries Minister Tony Ludwig proposed the laws at a Labor Caucus meeting this morning and it is has received strong support from the party.

Labor Senator Louise Pratt wrote on Twitter after the caucus meeting today: ''Pleased that Australia is giving the super trawler the boot out of Australian waters.''

The presence of the 142-metre trawler, which has been labelled a ''fishing factory'', has triggered strong protest by environmental groups.

media_camera Environmental laws do not legislate for vessels of the super trawler Abel Tasman's size. Picture: Ivon Perrin

Mr Burke has already brought in regulations on the Abel Tasman to stop dolphins and seals being killed as bycatch when fishing in Australian waters.

But Seafish Tasmania, which intends to use the trawler, which was originally named the Margiris, to fish for 18,000 tonnes of red bait and mackerel, said banning the super-trawler will cost 50 jobs.

In a statement, the company's director Gerry Geen said 45 of the jobs will be lost in the struggling Tasmanian town of Devonport.

"It is going to be hard to have to tell those employees, some of them who were long-term unemployed, that we no longer have a job for them," Mr Geen said.

He said the company was "extremely disappointed" at the government's decision.

"It seems that after we have met every rule, regulation and request made of us, after years of working with the relevant authorities, that in the end the government reacted to the size of the Abel Tasman and not the size of the quota and the science that supports it," Mr Geen said.

He said Seafish and its partners were examining their options and would wait until they saw the legislation before commenting further.

Earlier the company said it would continue fishing despite the tough new regulations - triggering the proposed law change.

Tasmanian Chamber of Commerce and Industry chief executive Neil MacKinnon said politicians were placing themselves above the scientific experts.

''(The Australian Fisheries Management Authority's) science is being sacrificed on the altar of populism,'' Mr MacKinnon said in a statement.

The trawler, which uses 600-metre nets, is currently docked in Port Lincoln, South Australia, and was expected to resume fishing soon.

Government backbencher Rob Mitchell acknowledged recreational fishers were worried about stock depletion.

But he said he generally had always been a big supporter of commercial fishing.

''Australia's got one of the best managed fisheries in the world," Mr Mitchell said, adding he had not seen the science on the impact of a super trawler.

The 13 organisations making up the Stop the Trawler Alliance, an unlikely coalition of green and recreational fishing groups, joined cyber-activists GetUp in celebrating a victory.

Greenpeace, which tried to block the ship from docking in Port Lincoln, labelled the Government's decision ''courageous.''

''Thousands of people across the country turned out to rallies, sent letters to editors, and pressured their local MPs. More than one person signed the Greenpeace 'No super trawlers' every minute,'' Greenpeace head of campaigns, Ben Pearson, said.

Paul Oosting from GetUp, whose website petition attracted 90,000 signatures, said the ship would have devastated local fisheries and impacted on protected species.

''Under the proposed conditions for fishing, the super-trawler could have legally killed up to 10 seals a day,'' he said.

''That is not acceptable.''

Tuna Club Tasmania's Neil ''Nobby'' Clarke added: ''Right from the start we believed that this vessel outdated the harvest strategy.

''The sheer efficiency of this vessel means that the science needed to be rock solid.''

The Opposition will wait to see what the government is proposing before responding.

Originally published as 'Marine science trashed by Burke'