Farmers "take a level of responsibility, but are not taking all the blame", for rising nitrate levels in Irish waters, the Irish Farmers' Association (IFA) has said.
The European Commission is to prosecute the State for failing to stop nitrate pollution from farms affecting rivers and lakes.
The Commission said the Republic was the only member-state not to have designated any nitrate-vulnerable zones, despite evidence that many inland and coastal waters were affected by pollution.
A spokesman for the IFA said: "We are not saying farming is not to blame . . . We don't accept the level of blame that is pointed at farmers. There is a lot of evidence that farming is operating under strict guidelines [on pollution]".
Furthermore, he said other faster-growing sectors were contributing to rising nitrate levels. These included the construction of holiday homes without adequate waste treatment, and the growth in towns, which produced more waste.
Ten years ago, EU member-states approved the European Nitrates Directive requiring all countries to identify nitrate-polluted waters within two years and designate vulnerable zones.
Action programmes to control nitrate pollution from farms were to be drawn up by the end of 1995.
A statement from the Department of the Environment said the zones would be designated by the end of this year. It also said a code of practice issued to farmers in 1996 contained detailed guidelines on protecting water quality.
"A series of measures has been progressively introduced over the years to provide additional protection for water quality and the environment generally against pollution from farming activities: additional measures continue to be developed."
An EPA report, Water Quality in Ireland, 1995-1997, said: "Agricultural fertilisers and farmyard wastes have been identified as the chief causes of nitrate enrichment of waters in many countries in Europe".
The report added: "The level of nitrate enrichment in Irish surface waters is generally low and well within the limits set for drinking water".
But it also said there is "evidence for a continued upward trend in nitrate levels" in rivers and streams in the south-east.
A recent EPA report on the quality of major estuaries and bays identified 17 sites that may be enriched by nitrate pollution.
Dr Padraic Larkin, director of the EPA, said a "significant portion" of this enrichment was believed to come from agricultural sources.