The Geelong Star is a large scale factory fishing vessel approved by the federal government to fish for small pelagic species which include mackerel, sardine and redbait from Brisbane down to Tasmania and across to Perth.

However, according to Australia Recreational Fishing Foundation managing director Allan Hansard, the trawler has chosen to catch its quota in places popular for recreational fishers, including off the coast of Bermagui, Narooma and Batemans Bay.

Mr Hansard believes even just the sight of the boat close to shore in these popular areas is driving tourists away.

"Whether the boat fishes all the fish out of the sea or not, there's an increased perception that it is fishing there and recreational fishers don't want to go there," Mr Hansard said.

"Tackle stores around Batemans Bay are concerned the boat fishing in those areas is stopping people coming down to the area to fish."

While the super trawler has "move on" provisions in place, Australian Recreational Fishing Foundation board member John Burgess said they were not strong enough to stop it depleting local fish stock.

While the small pelagic species aren't targeted by other fishing industries, commercial or recreational, they are considered bait fish that help encourage other, large species to come closer to shore. These could be migrating whales, dolphins or recreational catches like marlin or tuna.

Mr Burgess said even he had reconsidered a fishing trip down to the far south coast.

"The number of people who would normally travel from Victoria or from Sydney, the people who travel long distances with big boats, are just not going down there."

He said the cost for him to trailer his boat down to Narooma, plus accommodation, was too much to risk.

"I'm not prepared to go and spend that money if there is nothing there to catch," he said.

An Australian Fisheries Management Authority spokeswoman said fisheries were a shared resource where both commercial and recreational fishers needed to co-exist.

"There is no evidence to suggest that fishing by the Geelong Star impacts directly or indirectly on species important to recreational fishers," the spokeswoman said.

"Naturally, both commercial and recreational fishers will concentrate their fishing in areas and at times where they are most likely to catch the fish they are after. In the small pelagic fishery, one of the known fish aggregations occurs off the south coast of NSW."

The spokeswoman said Seafish Tasmania, the operators of the super trawler, agreed in May to avoid "key recreational fishing areas at peak times of the year".

The Geelong Star is one of the most heavily monitored boats in the Australian Fishing Zone. It is the largest of three vessels currently operating in the small pelagic fishery, and was approved to fish in Australian waters last year with a quota attached to its conditions.

A Senate inquiry report into the environmental, social and economic impacts of large-capacity fishing vessels commonly known as super trawlers operating in Australia's Marine Jurisdiction is due in November.