The Federal Government has decided to impose a two-year ban on super trawlers, undermining plans by the operators of the Abel Tasman to begin commercial fishing.

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

That has now been extended for 24 months to allow time for an expert panel to consider the environmental impacts of large-scale trawlers.

"The challenge here has always been that a vessel of this nature had never been used in Australian waters," Mr Burke told reporters in Canberra this afternoon.

"It did carry additional environmental challenges where, on a number of occasions, the information that I sought was not available.

"There was significant uncertainty about what the environmental consequences would be."

Seafish Tasmania brought the trawler from the Netherlands to Australia earlier this 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 last month, 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.

"With catch limits in place, there is no evidence that larger boats pose a higher risk to either the fish stock or the broader marine ecosystem," AFMA chief executive James Findlay wrote in September.

Treated 'unfairly'

Seafish Tasmania had flagged the potential for legal action if the Government decided to impose a two-year ban on large trawlers.

In a statement released late this afternoon, the company says it has been treated unfairly by the Government.

A spokesman says the company is consulting with its joint venture partner on its next course of action and all options are on the table.

When asked today about the prospect of having to pay compensation to the operators of the Abel Tasman, Mr Burke replied: "We believe we're on strong legal ground."

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

"The Government is right to take a precautionary approach, because monster boats like the Abel Tasman have no place in our waters," Greenpeace spokesman Ben Pearson said in a statement.

The Greens also welcomed the announcement, but Tasmanian senator Peter Whish-Wilson says he is concerned other fisheries may be open to the Abel Tasman.

"There are other fisheries, both in the state water such as the sardine fisheries that it could fish, and potentially in mackerel," he said.

"There is a possibility, but we'd be very surprised if the Minister let that happen given he obviously also expressed concerns over by-catch, particularly with seals and dolphins and penguins."

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

"All of the credible science... supported the sustainability of this fishery," said Coalition fisheries spokesman Richard Colbeck.

"That Mr Burke constructed his own uncertainty by not talking to any of these leading institutions is yet another indictment on the decision-making processes of this Gillard government."