A Tasmanian company that lost its bid to operate one of the world's largest fishing trawlers in Australian waters has received preliminary approval to fish a revised quota in a smaller ship.

The Parliamentary Secretary to the Minister for Agriculture, Senator Richard Colbeck, has announced Seafish Tasmania's 95-metre ship Geelong Star will be eligible to fish once authorities have approved a vessel-management plan.

The plan aims to ensure minimal interaction with marine mammals and seabirds, but can not be finalised until the Fisheries Management Authority has inspected the boat.

Late last year the Federal Government banned so-called super trawlers, which it defined as ships longer than 130 metres.

That followed a temporary ban in 2012 to block Seafish Tasmania from using what was then the world's second-largest trawler, the MV Margiris - later renamed Abel Tasman, to fish an annual quota of 18,000 tonnes of jack mackerel and redbait from an area stretching from Western Australia to Queensland, past Tasmania.

Conservation and recreational fishing groups have had long-standing concerns about the impact of large commercial trawlers like the MV Margiris on fish stocks.

But Seafish Tasmania maintained that quotas are set at sustainable levels.

Senator Colbeck said the Geelong Star's quota has been set at 16,566 tonnes for jack mackerel, redbait and blue mackerel for the 2014-15 fishing season.

But Nobby Clark from Game Fish Tasmania said he was nervous about the latest proposal.

"The questions that have been asked by our peak bodies have still not been answered around the series of effects of localised depletion and what these effects could possibly have on an ever-growing game fishing industry on the east coast of Australia," he said.

Senator Colbeck said research showed localised depletion was unlikely.

"Because most small pelagic species are highly mobile and local areas replenish quickly provided the overall stocks are not depleted," he said.

Mr Clark said he was anticipating a fresh wave of protests.

"It was never about the length of the vessel, it was about the efficiency of freezer vessels being able to take large quantities of fish out of localised areas," he said.

"We have seen the impact little vessels have had in the past."

A group representing Seafish Tasmania welcomed the decision.

Grahame Turk from the Small Pelagic Fishery Industry Association said the ship would have to come into port more frequently but could still work as efficiently.

"It's great news that we're able to now access a fishery that previously couldn't be fished," he said

"It's a sophisticated boat, it's got exclusion devices to minimise the impact on seals and dolphins and the like.

"People seem to take exception to large boats in excess of 130 metres so we're happy to go along with the Government's view that 130-metre boats plus should not operate in Australian waters."