One of Australia's largest fisheries is backing a plan for a super trawler to fish the nation's southern waters.

Conservationists and many fishing crews are fighting the proposal for the Dutch-owned FV Margiris to take fish, including redbait and jack mackerel.

Southern Bluefin Tuna Association CEO Brian Jeffriess said the trawler could set up opportunities such as providing feed for tuna farming.

He said the operation would be tightly controlled under scientifically-set quotas.

"It's taking a big risk. Now people who take that type of risk should be welcomed rather than criticised," he said.

Mr Jeffriess said it was unlikely the tuna industry would benefit in the short term from the trawler's arrival.

"The method of catching by this boat makes it doubtful whether it could be suitable for tuna feed so we're not so interested in that," he said.

"But what we're interested in is development of South Australian resources in the Great Australian Bight and frankly this is the best trial - experimental way - to show whether it can be best utilised or not."

'Mockery'

The prospect of the trawler's arrival has been criticised by Ceduna Mayor Allan Suter, on the west coast of South Australia.

He said the trawler's prospective catch would make a mockery of marine park plans outlined by federal and state governments.

"Bringing in a super, super vessel that has 40 crew and can catch thousands of tonnes of fish in a single trip ... that to me is the ultimate hypocrisy," he said.

"We are very disturbed about the level of restrictions that are being imposed on our fishers and to see something like this happen is unbelievably foolish."

Greenpeace has launched a petition calling for all such boats to be banned from Australian waters.

It says they are not normal fishing boats, but floating factories which have plundered other fisheries.

A Federal Government official says marine parks and the trawler's planned operation in Australian waters are separate issues.

She said Australia had some of the most sustainable and best-managed fisheries in the world, with strict Government regulations.

Although no application has been made for FV Margiris operate in an Australian fishery, quota management, by-catch provisions and strict observance would be applied if it arrived.

"The impact created by the new marine reserves on Australian commercial fishing is minimal, with approximately 1 per cent of effort impacted nationally," the government official said.

"The Government is working with the commercial sector on a fisheries adjustment package."

The Margiris is due in Tasmania at the end of the month and will be based there while it trawls an 18,000-tonne quota for jack mackerel and redbait.

Conservationists and anglers in Tasmania are concerned about over-fishing and have been fighting to stop the ship operating in Commonwealth waters.

Seafish Tasmania rejects the concerns, saying its quota for jack mackerel is only 5 per cent of the fishery.

The Tasmanian Greens have raised concern the factory ship may have access to Commonwealth Marine Protected Areas.

They say there is no way the jack mackerel and redbait fishery can remain sustainable if the trawler is allowed into reserves.