The Irish Farmers Association (IFA) is threatening to withdraw its support for social partnership unless amendments are made to the EU nitrates directive.
Farmer are opposed to the rules governing the amount of fertilisers they may use on their land which they claim are unworkable in their present form.
The EU has granted Ireland a deferral of that section of the directive which covers fertilisers to allow the matter be resolved.
But IFA President Padraig Walshe said today that despite impressions to the contrary, Minister for Environment Dick Roche had not engaged in "meaningful consultations".
He said: "Partnership is a two-way street and the Government was introducing highly-damaging legislation that would do nothing to improve water quality, which is the objective of the Directive."
He said the Minister was now blaming farmers for the fact that the regulations had not been introduced earlier and he accused Minister Roche of being disingenuous in his tactics.
But a statement from the Department of Environment this evening said Minister Roche has consulted extensively with the IFA and other farming organisations with regard to the Nitrates directive.
It continued: "Both Minister Roche and the Minister for Agriculture and Food, Mary Coughlan, have made it clear on a number of occasions that if revised phosphate tables are brought forward and supported by robust underlying science, then the Government is prepared to make a case to the European Commission for revising the current limits."
The EU directive is designed to limit the amount of pollutants, particularly nitrates and phosphates, from entering groundwater and inland waterways.
The Environmental Protection Agency estimates that 20 per cent of groundwater has nitrate concentrations above EU directive levels, while 27 per cent of rivers are affected by eutrophication (excessive richness of nutrients).
The pollutants come from
poorly managed town sewerage systems and from agricultural fertilisers.
The IFA has strongly criticised the advice given by Teagasc, the agriculture and food development authority, to the Government in advance of the introduction of the directive.
The Association boycotted Teagasc's National Tillage Conference in Carlow today in protest.
Fine Gael's agriculture spokesman Denis Naughten claimed today that the Government either did not have a clue about the implications of the Nitrates Directive or it just does not care.
He said the Taoiseach's claim that Ireland had obtained a satisfactory outcome in its negotiations with EU the directive "absolutely beggared belief".
Mr Naughten said: "Part of the action plan is suspended due to the lack of scientific support."
"And secondly, the other elements of the plan were introduced last night without any information being supplied to farmers on how to comply with the new rules," he claimed.