The company behind the super trawler Abel Tasman wants to use a smaller ship but says it cannot get Government advice about whether it can proceed.

The Federal Government has announced a two-year ban on super trawlers in Australia.

Seafish Tasmania director Gerry Geen has told Radio National the ban has left the company in the dark.

Mr Geen says he has been unable to find out if his company can fish its quota using a smaller factory freezer trawler of at least 90 metres.

"It's a very uncertain time for us and what we really need here is some advice from Government about what is acceptable and then we can make new plans as to whether it's feasible to bring in a vessel to catch our quota," he said.

"We've been trying to engage with the Government on this for weeks and nobody will talk to us.

Space to play or pause, M to mute, left and right arrows to seek, up and down arrows for volume. Listen Duration: 7 minutes 10 seconds 7 m Gerry Geen talks to Radio National's Fran Kelly Download 3.3 MB

"We need to fish our quota, we are a fishing company but we are not going to bring a vessel halfway around the world again without some concrete guidance."

Mr Geen says the company is millions of dollars out of pocket and if it can not get advice from the Government on what vessel to use, it will consider its legal options.

"We'd be prepared to look at compromises and we've been saying that all along," Mr Geen said.

"We prefer not to go down the legal route, that's the very last option so we would prefer to talk to the Government and work something out whereby we can fish our quota."

Seafish Tasmania sparked a community backlash when it brought the super trawler Margiris, re-named Abel Tasman, to Australia to fish an 18,000 tonne quota of jack mackerel and red bait.

In response to concerns, the Federal Government placed an interim ban on super trawler fishing but has now formalised a two-year ban to allow for more studies on fish stocks.

The 142-metre Abel Tasman remains in dock at Port Lincoln in South Australia.

Greenpeace is alarmed the company wants to use a smaller boat to fish its quota.

Spokesman, Nathaniel Pelle, says a 90 metre boat could use the same sized net as the Abel Tasman.

"The idea that you could reduce the size of supertrawler by about 13 metres and make it acceptable is pretty far fetched.

"There were a lot of problems with trying to bring the super trawler here in the first place. Stock assessments around the species they were targeting were uncertain," said Mr Pelle.

Advice 'ignored'

A marine scientist who advised the Federal Government on plans to ban super trawlers says it appears to have ignored his advice.

Professor Colin Buxton told the Government to approve the Abel Tasman, but closely monitor its activities.

The University of Tasmania's director of Fisheries, Aquaculture and Coasts, Colin Buxton, says the research will be inconclusive.

"It's nonsensical to say, 'we're going to ban the trawler for two years and get more science on the impact of trawling on seals and dolphins'," he said.

"How are you going to collect the data?"

Professor Buxton believes it is a political decision.

"For them to use science as an argument is wrong."

"We've got some amateur fisheries scientists who have come out of the woodwork and done their own analysis.

"They've created their own figures and unfortunately own our politicians have decided to take their advice ahead of their established scientific and reputable organisations."