A company which wants to operate a super-trawler in Australian waters vowed on Wednesday to fight an environmental ban set to be imposed by the government on the giant vessel.

Parliament Wednesday passed legislation which could prevent the 9,500-tonne, 143-metre (469-foot) Abel Tasman from operating in Australian waters until more scientific research is completed, a process which could take up to two years.

But Seafish Tasmania, which wants to licence the super-trawler to fish in Australia, said it would fight the matter, saying Environment Minister Tony Burke's intervention to stop the vessel was discriminatory.

"If the government thinks we'll just walk away, they are wrong," Seafish Tasmania director Gerry Geen said in a statement cited by the ABC.

"We understand there are a number of legal and other avenues still open to us, including the option of going fishing."

The super-trawler arrived in Australia last month as part of a joint venture between Seafish Tasmania and a Dutch company with a view to trawling in the waters off the southern island state for baitfish.

But it has been unable to fish after a campaign led by Greenpeace and local fisherman prompted Burke to amend laws on environmental protection and biodiversity conservation.

The Senate passed the amendments on Wednesday which give the minister greater powers and could prevent the vessel from trawling Australia's oceans until scientific research into its impact is completed.

"The sorts of powers that are made available legally by this bill going through are similar to legal powers I already had on land," Burke said.

"My priority is to make sure that we look after the environment."

Burke's amendments were rejected by the conservative opposition, but they were passed by the upper house after some concessions from the government, including a review after 12 months.

Greenpeace led the campaign against the huge vessel, taking a series of blockade actions in both Australia and the Netherlands, on fears its haul could include threatened species in its by-catch and deplete fish stocks.

Fisheries authorities have 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.