The company bringing a controversial trawler to Tasmania has defended the vessel's proposed new name and revealed it may change its travel plans.

The 142-metre FV Margiris is docked at Port Lincoln in South Australia where it is waiting to be approved as an Australian ship.

Seafish Tasmania has previously said the vessel would base itself in Devonport before fishing its 18,000 tonne quota.

But a company spokesman says the trawler may now go straight out and start fishing in Commonwealth waters without first docking in Devonport.

The Margiris has been criticised by Greenpeace and recreational fishers, who are worried the ship will deplete fish stocks in Commonwealth waters and will catch a large number of other species.

The company says the net will have underwater cameras attached, so the Australian Fisheries Management Authority can monitor by-catch.

However, the factory trawler cannot catch Seafish Tasmania's quota until it has been reflagged.

Destructive or sustainable? The size of the Margiris, now named Abel Tasman, has sparked fears it will decimate fish stocks. But Australia's fishing regulator says the trawler's quota is based on sound science. So will the super trawler devastate a region, or will its catch be a drop in the ocean?

Seafish has applied to have the trawler reflagged and renamed the Abel Tasman and hopes to be granted approval by authorities tomorrow.

The bid to rename the vessel angered independent Tasmanian MP Andrew Wilkie.

"To now use that man's name which has such an important historical significance in this state, it's almost a final insult," he said.

Seafish director Gerry Geen defended the decision.

"We're in a partnership with a Dutch company so we think it's an appropriate name," he said.

It is common for ships to be renamed when they are registered in new countries.

According to shipping databases, the Margiris has previously been called the Annelies Ilena, the Atlantic Star and the Siberian Enterprise.

Seafish Tasmania has also defended moves to bring a European expert to Australia to examine the super trawler.

Mr Geen says the expert will look at the device preventing bycatch, but says the move does not suggest there's a problem with the nets.

"No, absolutely not. This is us just being double safe," he said.

"We take the issue of marine mammal interactions very, very seriously and we want to make sure that we do our very utmost to ensure that those interactions don't occur."

Seafish Tasmania expects other species will make up 1 per cent of the factory trawler's catch.