The rapid spread of a pathogenic parasitic worm which infects the bladder of the eel is causing concern among scientists who have prepared a report on eel fishing in the Shannon for the ESB.
The parasite, known as Anguillicola crassus, infects the swimbladder of the eel and is spreading through the State's eel fisheries.
According to the scientist who compiled the report, Dr Kieran McCarthy, the danger is that this and other species introduced to the Shannon may have a severe impact on the eel population.
In his report, Eel Fishing on the River Shannon, Dr McCarthy expressed concern about the steady decline in the eel population of the Shannon estuary.
He said declining European eel stocks over the past 30 years had affected natural recruitment from the Sargasso Sea spawning area to Irish eel fisheries.
His report recommended measures such as a programme of stock enhancement involving the capture of juvenile eels in the Shannon estuary for stocking lakes.
The report said the 35 part-time fishing crews working in the Shannon catch 80 tonnes of eels each year, generating a combined revenue of about £250,000.
The report concluded that the Shannon estuary area could sustain increased fishing.
However, it warned that matching the level of the Lough Neagh fishery, which produces about 800 tonnes annually, would require a major long-term investment programme.
The report also recommended improved monitoring of the man-made barriers to eel movement.
It called for research on the feasibility of building passes to assist movement in the Shannon estuary area.
That recommendation could open the rift between the commercial fishing industry and the ESB, which controls eel fishing on the Shannon.
The fishermen argue that the ESB is only interested in generating power from the waterways.
The company denies that.