A report on the water quality of Lough Conn claims a sewage treatment works and urban drainage near Crossmolina, Co Mayo, are the main pollution threat.
Previously agriculture had been named as the biggest cause of damage to one of the west of Ireland's prime freshwater lakes.
The report contradicts the findings of the 1992 Lough Conn report, commissioned by Mayo County Council, and a recent report by the Environmental Protection Agency (EPA) which claimed that the farming industry, notably agricultural run-off, was responsible for the high phosphate levels in the lake.
The latest report, prepared by Mr John Mulqueen, from Teagasc, rejects claims that a deterioration in the water quality of Lough Conn is because of phosphate enrichment.
It recommends that the Lough Conn report "should be reviewed and revised".
Surveys for the 1992 report claimed that excessive phosphate levels which gave rise to pollution were believed to be "due to agricultural run-off . . . from field surfaces and/or farmyards".
In the new report, Mr Mulqueen says no field evidence is advanced to support this and the sewerage works near the lake is "the only continuous source of contaminants (including phosphorus)."
His findings have been rejected by the EPA, the North Western Regional Fisheries Board and Mayo County Council.