Minister for Agriculture, Food and the Marine Charlie McConalogue told the European Commissioner for the Environment that the timeline for implementing the cut in the nitrates derogation was “difficult to explain from a scientific point of view”.

In a letter to Commissioner Virginijus Sinkevicius, the minister also told the commissioner that the mapping process of areas where water quality was deemed poor enough to warrant a cut in the derogation included “a number of anomalies”.

As things stand, the maximum level of organic manure nitrogen (N) stocking rate under the derogation will fall from 250kgN/ha to 220kgN/ha from January.

Since it emerged in early September that the European Commission would not revisit the conditions of Ireland’s nitrates derogation, Minister McConalogue has come under fire from several quarters.

Some farm organisations and politicians have claimed that he did not press the commission to seek measures to mitigate the impact of the derogation cut.

However, the letter from the minister to the commission, dated before the announcement that the commission would not revisit the terms of the derogation, indicates that the minister did outline concerns to the environment commissioner; while seeking more time to asses the effects of water quality improvement measures undertaken in Ireland.

Minister McConalogue told the commissioner that there are “good reasons to reconsider the proposed reduction”.

He also said: “It is now evident in the light of experience, and having regard to the global impact of the illegal invasion of Ukraine by Russia, that this reduction, so soon after the granting of the derogation, will have a number of unintended consequences.

“It is now evident that the anticipated reduction in the organic nitrogen allowance is fueling land price inflation. Increased demand from derogation farmers seeking to mitigate their income-loss is effectively excluding tillage farmers, many of whom depend on rented land, from the market.”

The minister also warned the commissioner that, in circumstances where additional land is not available, some dairy farmers may seek to avoid organic nitrogen limits by moving away from a grass-based outdoor system.

Minister McConalogue said the measures to improve water quality, agreed as part of the current nitrates derogation, “have not been in place long enough to demonstrate their full impact on water quality”.

“The effectiveness of these measures depends on factors such as the existing source levels, climate, soil type, catchment scale and nutrient flow paths, and inevitably involves a time lag to determine if there has been an impact on water quality,” he added.

“The application of such a significant reduction in organic fertiliser allowances, within a timeframe which is difficult to explain from a scientific point of view, is likely to alienate whose we most need to support our efforts.”

The minister’s letter went on to point to “anomalies” in the mapping process that will inform the reduction in organic nitrogen allowances.

For example, the minister said that the area of the country that will see the derogation reduced includes some areas with “very low nitrate levels in water” and some area where “agriculture is not deemed to be a significant pressure on water quality”.

On the other hand, the map excludes some areas with higher average nitrate concentrations, where nitrate levels are a pressure on water quality, according to the minister.

“Taking all of this into account, I am asking for more time to assess the impact of the additional measures adopted in the context of Ireland’s Nitrates Action Programme (NAP), before any decision is taken in relation to nitrogen limits.”

The minister told Commissioner Sinkevicius that he was prepared to consider what further mitigating measures might be taken to improve water quality.

He said: “I strongly believe that an approach that uses the best available science and brings the farming community on that journey is necessary to deliver the best outcome for water quality.”

The letter from Minister McConalogue to the environment commissioner also included an invitation to the latter to visit Ireland “to witness first-hand the work being done to improve our water”.