Seafish Tasmania has lost its second bid to use its super trawler in Australian waters.

Federal Environment Minister Tony Burke last night moved to ban Seafish Tasmania from using the Abel Tasman, formerly called the FV Margiris, as a "floating freezer".

Mr Burke's intervention comes in the middle of the Australian Fisheries Management Authority assessment of Seafish's transhipment proposal.

Under the proposal, the 143-metre long mid-water trawler would never need to cast its nets. Instead smaller vessels would catch Seafish's quota of red bait and jack mackerel and unload the fish on to the super trawler to be processed in its freezer storage area.

"While from the company's perspective what they have put forward is a compromise on their fishing method, the environmental consequences are similar to those which concerned me with their first proposal," Mr Burke said yesterday.

"This government takes a highly cautious view when it comes to protecting the ocean. We take ocean protection seriously."

Seafish Tasmania has not ruled out trying to use a smaller vessel with freezer storage capacity or taking legal action after the government rushed through legislation to stop the controversial vessel fishing in Australian waters in September.

Mr Burke was alerted to Seafish's plans in November and sought advice from his department about its legality and his powers to intervene.

Transhipment is not covered in the original "declaration", which prevents the super trawler fishing, forcing Mr Burke to begin a new "declaration" process to block it.

The company now has six weeks to formally respond before Mr Burke can extend the ban for up to two years while scientific work is carried out on the environmental impact of the new method of fishing.

It's now unclear if the Greens will proceed with plans to move a motion calling on Mr Burke to close the loophole, which allowed transhipment to occur.

Tasmanian Greens Senator Peter Whish- Wilson was planning to move a motion next week urging Mr Burke to add "a method of processing, carrying or transhipment of fish" to the list of prohibited activities.

Senator Whish-Wilson said Seafish Tasmania had exposed a loophole in the legislation rushed through last year and it needed to be closed before AFMA concluded its assessment of the proposal.