the Margiris super trawler.

Conflict ... the Margiris super trawler. Photo: Greenpeace

Conflict over the largest vessel ever to fish Australian waters is intensifying, as key independent MP Andrew Wilkie steps up his challenge to the legality of its quota.

The 9500-tonne super trawler MV Margiris is to fish for mackerel and redbait offshore from New South Wales, south and around the coast to Western Australia.

Environment groups are mounting a national campaign against the ship, which is due to arrive this month, while recreational and tuna fishers have agreed to try to minimise its impact.

Mr Wilkie said today his investigation found the Australian Fisheries Management Authority admitted that, when advice was given for setting the 19,000 tonne annual quota, it had not given a "literal" reading of the law.

"AFMA has as good as admitted the fishing quota for the MV Margiris is not worth the paper it's written on," Mr Wilkie said. "So the quota needs to be ripped up and the whole assessment process started again.

"In light of this revelation, the MV Margiris may as well turn around and return to where it came from."

Mr Wilkie raised doubts over a potential conflict of interest in advice from an AFMA advisory committee. A member of the Margiris joint venture, Seafish Tasmania director Gerry Geen, was present when the advice to lift the quota was determined .

AFMA chief executive James Findlay told Mr Wilkie that, because any member of an advisory committee could be argued to have a conflict of interest, there was a "standing arrangement" to allow people such as Mr Geen to remain unless there was an objection.

Mr Findlay said this complied with the Fisheries Administration Act, but Mr Wilkie said the "standing arrangement" raised more questions than it answered, and AFMA appeared to have acted unlawfully.

AFMA has claimed strong scientific backing for its approach, but aquatic policy specialist Jon Nevill said the organisation's processes were fundamentally wrong.

Instead of taking the approach of considering the effect of fishing on the whole ecosystem, AFMA adopted a "single stock" concept, Dr Nevill said.

The authority maintains that fish stocks to be targeted by the Margiris are in excellent shape.

Total catch limits are less than 10 per cent of the fish stock, and Seafish said the Margiris's quota would amount to only half of the total catch limit.

The Tasmanian Greens called on Fisheries Minister Joe Ludwig to rule out fishing in existing Commonwealth marine reserves, where mid-water trawling has not been banned.

In response to Mr Wilkie, AFMA chief executive James Findaly said he was confident that the fishery was lawful.

"The decision on catch limits rests with the independent, expert group of AFMA commissioners," he said.

The Dutch-owned Margiris left the port of Abidjan, Cote D'Ivoire, in West Africa this week.