A Tasmania Police spokesperson confirmed a 39-year-old man from the Philippines was working aboard a fishing vessel operating out of Victoria.

They said with poor weather conditions, strong winds and high swells they has been advised by experts that it was extremely unlikely that the man could have survived.

Scallop Fishers Association Tasmania president John Hammond was fishing in the area off the coast of Flinders Island on Thursday night when he received a call to assist with the search.

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Mr Hammond said he and his crew of the Shandra received a call from the owner of the Lady Miriam, the 72-foot trawler the missing man had been working aboard, to see if any ships in the area could assist.

"Our boat was out there scallop fishing and we got a request at about 8 o'clock to go and assist, but we were four hours away and it was pretty much impossible for us to help do anything," he said.

Scallop Fishers Association Tasmania chief executive Bob Lister said the Lady Miriam was not a scallop boat, and to the best of his knowledge was not a boat sailing out of Tasmania.

Mr Lister confirmed three scallop boats were operating in the waters east of Flinders Island with all three boats and their crews accounted for.

"There have been three Tasmanian boats scallop fishing in the area east of Flinders Island and at the moment there's one boat still there and there are two vessels that are in port in Tasmania," he said.

He said he understood the missing man was based out of Victoria with the Lady Miriam sailing out of Lakes Entrance in Victoria.

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According to Mr Hammond, the incident took place about 40 kilometres east of Babel Island and said by the time they reached the search area, with heavy seas and wild weather the chance of locating the man alive was slim.

"The waters were 12 degrees, and with the wind blowing a gale, you've got about 20 minutes in the water at that point," he said.

"There wasn't much we could do and they called off the search at two or three o'clock in the morning."

Mr Hammond said despite the situation fishermen going overboard was highly uncommon, but the risk was always present.

"We hardly ever lose any crew over the side of our boats, they're very safe these days," he said.

"Unfortunately big seas have come and took him over the back by the sound of it."

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Mr Hammond said the accident was a simple instance of being in the wrong place at the wrong time.

"Unfortunately, it's a dangerous game, fishing is recognisably one of the most dangerous jobs in the world," he said.

"You get yourself in the wrong place at the wrong time and it's always there, that possibility that when you leave the wharf, turn the engine on and go fishing there's no guarantee you're coming back.

"Luckily 99 per cent of the time you do come back - but there ain't no guarantees."

Mr Hammond said although he did not know the man, the incident had resonated with the local fishing community.

"Of course, we feel very sorry for the family because we're all at risk all the time and now we know how this would affect us if one of our guys went overboard," he said.

The police spokesperson said a report would be prepared for the Coroner.

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