A 36-year-old man from Pomona in New South Wales' far west has allegedly fished more than 12 tonnes of protected golden perch from the Darling River over a 20-month period.

Key points: In NSW, golden perch are protected from commercial fishing

In NSW, golden perch are protected from commercial fishing Authorities from three states involved in investigation

Authorities from three states involved in investigation Man faces maximum penalty of $110,000 and appears in court in June

The fish with an estimated value of $200,000 were allegedly sold to Victorian fish markets under the guise of having been obtained legally in South Australia.

The NSW Department of Primary Industries, Victorian Fisheries Authority and Primary Industries South Australia apprehended the man on March 13, seizing his boat, motor and trailer, seven illegal gill nets, the illegal fish and a mobile phone.

"This should send a clear message to anyone considering exploiting this valuable resource for personal gain that it will not be tolerated," said NSWDPI Compliance Director, Patrick Tully.

Fisheries authorities teamed up with NSW police to obtain a search warrant, which resulted in the seizure of a further 150 kilograms of golden perch, eight gill nets, four fire arms and ammunition.

Under New South Wales laws, golden perch are protected from commercial fishing, while recreational fishers are restricted to catching five perch per day and can only be in possession of 10 perch at any given time.

The ABC understands the man was using an expired South Australian fishing licence to avoid suspicion, since South Australia does not have the same protections for golden perch.

Authorities seized the man's boat, trailer and motor, illegal gill nets, fish, and a mobile phone. ( Supplied: NSW Department of Primary Industries )

'A slap in the face' for far west NSW

The illegal fishing allegedly took place in the Darling River near Menindee in the state's far west, an area recently devastated by mass fish kills.

Menindee resident Graeme McCrabb said it was a blow to fish repopulation efforts as 80 per cent of the golden perch population came from an important nursery area for fish at Menindee.

"It's just another slap in the face for the far west.

"The fish kills have highlighted how little interest politicians have taken in the far west and lower Darling, and now this."

Mr Tully said NSWDPI understood the frustrations of Menindee locals.

"Illegal fishing is a real kick in the guts for a community already doing it tough because of the drought," Mr Tully said.

"Our fisheries officers do a great job protecting our native fish stocks and legitimate aquaculture industry."

The man is facing a range of charges carrying a maximum penalty of $110,000 or a year in prison, and is due to face court in June.