The Tasmanian Parliament has passed a motion opposing the operation of a super trawler bound for Devonport in the state's north-west.

All three parties supported the motion put forward by the Greens opposing the Margiris which is due to arrive by the end of the next week.

Labor Member for Braddon Brenton Best told State Parliament the Margiris should not be allowed to fish in Commonwealth waters.

"It should be banned in Australian waters, I think it will threaten many jobs in Tasmania," he said.

"Whilst there's a promise of some 40 on the ship direct, I think it will cost Tasmania hugely in jobs with the damage that it's going to do."

The Commonwealth Ombudsman has launched a formal investigation into the Australian Fisheries Management Authority's allocation of an 18,000 tonne fishing quota to the Margiris.

The Greens' Kim Booth opened debate on the motion by saying the quota process was "dodgy".

Destructive or sustainable? The magnitude of the Margiris operation 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?

Resources Minister Bryan Green told Parliament the Government had requested more information about the process from AFMA.

"We as a state need to be satisfied that it's not going to have the impact that people are suggesting it will," he said.

"There is a difference with a respect to the fishery being fished by a number of vessels as opposed to just one vessel. That needs to be contemplated."

Mr Booth says tri-partisan support for the motion is a reflection of community concerns about the Margiris.

"This is, I think, a profound result," he said.

"It's a demonstration of how a cooperative parliament can work, that all three sides of parliament can come together to stand up for the best interests of their community.

The trawler will fish Commonwealth waters for jack mackerel and redbait but recreational fishers and environmentalists fear there could be localised overfishing.

Federal Environment Minister Tony Burke says he is seeking more information about the potential for animals like dolphins, seals and albatross to become by-catch.

Seafish Tasmania says the public concern over the trawler has been fanned by scaremongering by the Greens.

Subsidies claim

Greenpeace claims the company which owns the trawler receives millions of Euros in annual subsidies.

The 142-metre trawler is owned by Dutch company Parlevliet and Van der Plas.

Pavel Klinckhamers from Greenpeace says the Dutch company has received the equivalent of 39 million Euros since 1994, proving the trawler is not economically viable.

"Such a large trawler like the Margiris is not very efficient with fuel. It has to burn lots of fuel, for freezing capacity, for towing the big nets," he said.

Seafish Tasmania says the European subsidies will not apply to the Margiris while it is in Australian waters.

The company is confident the trawler will arrive in Tasmania by the end of next week.