Federal Environment Minister Tony Burke has announced he will knock back Seafish Tasmania's latest application to use its super trawler as a floating freezer.

Seafish Tasmania announced last month that it wanted to use the Abel Tasman a floating freezer.

The company said it wanted to buy jack mackerel and red bait from smaller boats. The fish would then be taken onto the Abel Tasman to be frozen and stored.

It put forward the proposal after Mr Burke banned it from trawling for two years last November.

Mr Burke has told Lateline he has received the environmental impact study and he is not satisfied with the new proposal.

"Even though it sounds like they're not putting the net out, there's no problem, the advice that came back for seals and dolphins and localised depletion, the problems that arise are exactly the same. For seabirds, the problems are potentially worse," he said.

He says floating freezer proposal is not a good enough compromise.

"It's a new fishing activity and yes, even though it looks like a compromise on the face of it, a whole lot of the environmental problems we had last time are replicated again under this so called compromise model," he said.

Mr Burke issued an interim 60-day ban last September in the face of a strong community campaign against the ship.

The ban was then extended for 24 months to allow time for an expert panel to consider the environmental impacts of large-scale trawlers.

Seafish Tasmania brought the Abel Tasman from the Netherlands to Australia last year to fish for a near 18,000-tonne quota of jack mackerel and redbait, believing it had the support of the Government.

Speaking to the ABC's Four Corners program aired in October, the company's director, Gerry Geen, said no-one in the Government tried to stop the Abel Tasman coming to Australia despite the concerns of some environmentalists.

The Government's fishing regulator, the Australian Fisheries Management Authority (AFMA), had also defended the Abel Tasman's presence in Australia, arguing there was no reason to single out this particular ship.

Conservationists welcomed the Government's decision in November, saying the trawler would have "plundered" domestic fish stocks.

The Opposition, however, said the decision was a victory for politics over science.