Super trawler Abel Tasman has quit Australia but its backer says he expects it to return and fish within two months.

Seafish Tasmania managing director Joe Pirrello said the ship left Port Lincoln early yesterday afternoon but be did not know its destination, as the company had sold it.

But Mr Pirrello, who is based at Ulladulla in New South Wales, said he expected a legal challenge to  overturn the fishing ban on the Abel Tasman, paving the way for its quick return.

Mr Pirrello said the case - against the federal government, Environment Minister Tony Burke and Fisheries Minister Joe Ludwig - would start in the Federal Court in Brisbane on March 15, with a decision by the end of next month. 

He said the ship, or a smaller one, could immediately return, as  the Abel Tasman sale contract included an option to buy the ship back if the court case succeeded.

Mr Burke said he was confident of his legal position and it was him, and not Seafish, that was relying on science and protecting the oceans.

Seafish Tasmania last year brought the 142-metre ship to Australia to catch a yearly quota of 18,000 tonnes of jack mackerel and redbait in waters from Queensland to Western Australia.

But after a public outcry, Mr Burke initially banned the ship from fishing and then stymied a second proposal  for it  to be a floating freezer for a fleet of smaller boats.

Mr Pirrello said that latest rejection had made him think that Mr Burke was more motivated by winning votes than heeding science.

Mr Pirrello said Seafish had been working on a fishing plan for 12 years and he believed his case was strong in the upcoming court case, so he was not giving up.

``It's our hope to bring back the Abel Tasman by May,'' Mr Pirrello said. ``It's not an option not to come back.''

Mr Burke said the Gillard government last year stopped the Abel Tasman from fishing until sufficient scientific checks were done.

``I'm very cautious in making sure that we don't take risks with the ocean, and they (Seafish) don't want me to be cautious,'' Mr Burke said. ``We are very confident of our legal position.''