Greenpeace protesters have unsuccessfully tried to stop the world’s second-largest super-trawler docking at Port Lincoln, amid controversy over its alleged history of overfishing.

Crew members aboard the 9,500-tonne Dutch-flagged FV Margiris repelled attempts by Greenpeace to board the 142-metre vessel when it arrived in the South Australian port.

Activists were also forced away by a pilot ship from the port.

“The Greenpeace activists managed to get an inflatable (ship) between the pilot ship and the Margiris itself but pretty much got squashed out of the way pretty sharpish, Greenpeace spokesman James Lorenz said.

Seafish Tasmania intends to use the Margiris to fish for 18,000 tonnes of redbait and mackerel, a quota the company says has been backed by a group of eminent marine scientists.

But Greenpeace wants the Gillard government to refuse to grant a fishing license to the Margiris and to introduce a policy to ban super-trawlers from Australian ports.

Environment Minister Tony Burke has also expressed concerns about the amount of by-catch the trawler can snare in its nets.

A complaint by Tasmanian independent MP Andrew Wilkie has also resulted in a Commonwealth Ombudsman’s investigation into its quota.

Greenpeace Oceans campaigner Nathaniel Pelle said trawlers like the Margiris “literally vacuum up entire schools of fish, amid concerns about the depletion of southern fish stocks and the impact on sea birds, seals and dolphins.

“They have overfished European waters, collapsed fisheries in the South Pacific, and devastated fishing communities in West Africa. We simply can’t let the same thing happen in Australia.

Canberra is yet to give final approval for the Margiris to fish Australian waters, but the Australian Fisheries Management Authority (AFMA) has dismissed concerns about over-fishing.

Port Lincoln mayor Bruce Green also defended the ship and said the tools of the fishing industry had changed, becoming more sophisticated with locating catch and species.

“It’s not about whether you’ve got one ship or two, or 10 rather than one, it’s about what is the quota, what is the biomass, how can we target that and not do damage to other species? Mr Green said.

Australian Southern Bluefin Tuna Industry Association spokesman David Ellis said the local fishing industry supported the ship’s arrival, and was satisfied AFMA had introduced sustainable quotas and adequate checks to ensure it had a very low by-catch.

“This vessel is fishing on behalf of an Australian company; its going to be going out and fishing sustainably within fishery management plans, Mr Ellis said.

“It’s a new way of looking at how we can best meet the market demand of seafood – I think change is what confronts people.

South Australian Greens leader Mark Parnell said the issue was not just about quotas and numbers, but was also about the impact on communities and the environment.

“If you managed to suck all of the small fish out of the sea in a particular area, well there goes your big fish there goes the fish that the recreational fishers are targeting and other commercial fishers are targeting, Mr Parnell said.

“It’s not just about raw numbers over the whole of the South East of Australia, its also about localised impacts.

“It’s quite outrageous that were placing local jobs, local family operations, with one big overseas factory ship just sucking the quota out of the ocean in as short a time as possible, I think it’s obscene.

The Margiris is expected to stay in Port Lincoln for several days to be re-flagged as an Australian vessel, and undergo maintenance and government checks.