The High Court is to refer matters raised in a challenge taken by An Taisce for a judicial review of the Government's fifth Nitrates Action Programme to the European Court of Justice.
In a judgment, Mr Justice Humphreys said he has decided that he will be referring questions on the details of the case to the European court for consideration.
"The applicant has raised what are clearly novel, complex and important issues of EU law, culminating in a question regarding the validity of a Commission decision.
"The court doesn’t have jurisdiction to determine the latter issue in favour of the applicant, and isn’t particularly minded at the present time to determine it in favour of the respondents.
"While making a reference to the CJEU is generally optional apart from for apex courts, a case where the validity of an EU law measure is in issue can be an exception," he said.
An Taisce challenged the Nitrates Action Programme which permits Irish farmers to have higher levels of organic nitrates on their land.
The non-governmental organisation maintains the programme is not protecting water as it is meant to do.
Reacting to the development, An Taisce CEO Gary Freemantle said: "This judgment is a step towards ensuring that Ireland has the strongest possible legal framework to safeguard our waterways.
"This is directly connected to the An Taisce mission of protecting and celebrating Ireland’s natural and built environment for present and future generations."
President of the Irish Creamery Milk Suppliers Association (ICMSA) Denis Drennan welcomed the development.
"ICMSA is a notice party in this High Court case, our involvement stems from our conviction that retention of the Nitrates Derogation is absolutely crucial to the survival and wellbeing of Irish farming.
"ICMSA made substantial submissions and lodged affidavits on behalf of our members. And we welcome the court’s fair and balanced consideration of the farmer concerns as submitted by our lawyers," he said.
It is unclear how soon the European Court of Justice will begin consideration of the matters being referred.
