The nitrates plan sought by the EU from the Government is about the quality of drinking water, not just about farming, according to the Minister for Agriculture and Food.
Mary Coughlan said yesterday that while she was aware that farm organisations were not happy with the new plan being submitted tomorrow to the EU, failure to do this would result in court action being reintroduced by Brussels with the danger of fines being imposed.
Ireland has been seeking to minimise the impact of the Nitrates Directive on farming by seeking a derogation to allow farmers to apply more nitrogen on their land than the 170kg per hectare demanded by the directive.
"The problems have been exaggerated by Fine Gael because there are many farmers along the west coast and across the State who will not feel the impact of this at all," the Minister said.
"However, there are those who will, especially the intensive farmers and pig and poultry producers and those who have to store nitrates for 22 weeks. I will be meeting all the organisations involved over the next two weeks and we will be looking at these problems."
Ms Coughlan indicated that there might be additional grant aid for building storage facilities for those obliged by the plan to store nitrates for up to 22 weeks.
She said it had to be accepted that the document based on the plan drawn up by Denis Brosnan had been rejected and the issue was now back to a science-based approach.
The former managing director and chairman of the Kerry Group was appointed by former minister for the environment Martin Cullen last year to advise on the implementation of the directive.
"There may well be room to manoeuvre but the plan must be submitted on Friday or we face the consequences," she said.
Meanwhile, a Fine Gael group which met EU officials in Brussels were warned that a derogation would not be automatic and other member states would have to be convinced that it was warranted.
The delegation said senior officials dealing with its implementation had said that to obtain a derogation, Ireland would have to provide the scientific evidence that it was warranted and would have no adverse impact on the environment.
Fine Gael agriculture spokesman Denis Naughten said: "The procedures to be employed to obtain a derogation mean that it will take at least 12 months to secure such agreement. Also the fact that this Irish Government has not facilitated the construction of additional storage capacity will not help the case."
The European Commission made it clear that it was the Government, not the EU, which decided how the Nitrates Directive was implemented. Its only role was to ensure that that the directive was complied with.