In a report on the controversial plan, the federal government-appointed panel found a host of protected native seals and seabirds would be at risk of losing their food to the fishing, even if special precautions were taken.

"The panel's assessment has confirmed that there are considerable uncertainties relating to the extent of those impacts, and the level of impact that would create adverse environmental outcomes," the report released on Tuesday said.

The panel was asked to examine the fishery for jack mackerel and redbait by the previous Labor government after it banned the Dutch-owned super trawler Margiris when it came to Australia to fish an 18,000-tonne quota in 2012.

Prime Minister Tony Abbott said earlier this year that the supertrawler would remain banned, but the small pelagic quota holder Seafish Tasmania has entered the fishery for assessment of its sustainability by the independent Marine Stewardship Council.

The expert panel, chaired by fisheries management consultant Mary Lack, was asked to report to the Environment Minister, now Greg Hunt, on the proposal's effects on protected species, and whether it would cause localised depletion of the target fish.

The report found it was inevitable that the fishing would directly affect protected species of seals, dolphins and seabirds.

"Some interactions will result in mortalities regardless of the adoption of the best available mitigation and management measures; however, there remains uncertainty about the extent of those interactions," the report said.

Among species at greatest risk from localised depletion of their prey were fur seals, gannets, short-tailed shearwaters, little penguins and shy albatross.

But it concluded the localised depletion of small pelagic target fish was unlikely to affect the overall stocks of the fish.

The Greens' spokesman on fisheries, Peter Whish-Wilson, said the report vindicated opponents of the ship, including conservation groups and recreational fishers.

"The Greens have long argued that the science on the wider impacts were too uncertain for the minister to make a call on allowing this gigantic floating factory into our waters," Senator Whish-Wilson said .

"We are still a long way away from a point where we could be confident that industrial-scale fishing from a supertrawler wouldn't have these impacts."

The Commonwealth Fisheries Association was contacted for comment.

It has defended the use of large vessels, saying size and dimensions should not be a driving factor when it comes to fisheries management decisions.

A spokesman for Mr Hunt said the government was considering its response to the expert panel report, as it worked to develop a permanent solution.

A two-year ban on a supertrawler hauling its nets lapsed earlier this month, but a further ban on a supertrawler acting as a mother ship, receiving and processing fish, is in place until next April.