The Department of Agriculture has said that direct payments to farmers from the EU will not be at risk because of the failure of the Minister for the Environment, Mr Dempsey, to declare "nitrate-vulnerable" areas before January 1st.
That was the deadline set by the EU for the Minister to introduce wide-ranging controls on the use of fertilisers on farms to protect water quality in the State.
Ireland is the only member-state not to have designated any of its territory under the 1991 Nitrates Directive. Mr Dempsey had been expected to bring proposals to designate the areas to a Cabinet meeting before Christmas but that did not happen.
Farming organisations in the Republic have claimed that curbs on the use of nitrates and a lowering of stocking rates on farms if water quality does not improve in four years will render commercial farming uneconomic.
They have demanded that the Government enter into proper negotiations with farmers to limit the impact the curbs will have on their operations before any designations are made.