ICMSA president John Comer voiced concerns that they will lead to significant additional costs and may be impractical to put in place.
"In relation to roadways and water troughs, some farmers who followed the best advice available will now find that they will have to substantially alter their investments - at a considerable cost to themselves - to meet the regulations," he said.
Mr Comer stressed they understand the need to protect water quality but said some of the proposals do not make sense.
The review shows there has been an overall decline in nitrate concentrations in groundwater since 1995. However, since 2013 there has been a slight increase in nitrate concentrations nationally.
The EPA pointed out there has been an increase in maximum nitrate concentrations for 47pc of lakes, and five of 24 transitional and coastal water bodies have shown an increase in eutrophication.
"It is a bit too early to say whether the slight increases we are seeing are significant trends or not," an EPA spokeswoman said. However, they said the proposed steps, along with the proposals in the draft river basin management plan, should contribute to positive engagement with the farming community and improve water quality.
It stressed that a purely regulatory approach would not be as effective as one involving engagement with farmers.
The review highlights that as the industry continues to grow, it will be required to show more commitment to the principles of sustainability, recognising that gains in productivity must not be at the expense of the environment.
Just 10pc of grass soil samples and 12pc of tillage soils show overall good fertility, with two-thirds of soils nationally having a sub-optimal pH status, showing a need for lime on most farms.
"The current review of the rules surrounding the use and management of nitrogen and phosphorus on Irish farms provides a real opportunity to reverse decades of declining soil fertility levels," IFA President Joe Healy said.
He emphasised the chief priority must be the continuation of both the derogation for the dairy and livestock sector and the transitional arrangements for pig and poultry farmers.
The derogation from the 170kg livestock mature nitrogen limit is up for discussion with the Commission currently to see if Ireland can be allowed to continue to avail of it.
Less than 5pc of farmers in Ireland avail of the nitrates derogation.
"However, these farmers represent a cohort of progressive farmers who will underpin the development of the sector in the coming years," he said, adding these farmers face increased compliance obligations, administrative burdens and more likelihood of being inspected.
Mr Healy said to avoid imposing thousands of euro of haulage costs on pig and poultry farmers, the transitional arrangements must be extended, at least until the renewable heat incentive is introduced. He stressed vital policy support to deliver sustainable growth is required.
Some of the proposed changes to the Nitrates Action Plan
The review team highlighted that the proposed new action programme includes measures aimed at further strengthening the protection of water and delivering optimum soil fertility for efficient farming and effective water protection.
It found that the Nitrates Directive requires all Member States to define periods when the land application of fertiliser is prohibited and there was no scientific basis to support increased flexibility during the prohibited period.
* Bovine exclusion from watercourses on farms with grassland stocking rates above 170kg N/ha from January 2021, with watercourses to be fenced off. There are 12,350 farms with grassland stocking rates above 170kg N/ha. The review found this would allow vegetation to recover on banks
* Prevention of direct run-off from farm roadways to water from January 2021, with a road specification to be supplied. There are 15,500 specialist dairy farms, with typical farm roadway lengths of 1.4km per farm. There will be a range of options to prevent run-off including cambering the roadway, measures to reduce the speed of water flow and earth bunding along the road
* Livestock drinking points must not be located within 20m of waters on farms with grassland stocking rates above 170kg N/ha from January 2021
* Appropriate phosphorus build-up rates must be adopted for farmed soil
* Facilitate the use of pig slurry to meet phosphorus requirements. They would be required to be applied by low-emission slurry spreading technology
* Simplify the calculations of maximum fertiliser N and P allowance
* Implement a comprehensive Knowledge Transfer programme for farmers availing of increased phosphorus build-up allowances
* Collaborative approach involving State agencies and the farming sector be adopted to bring about behavioural change to achieve sustainable farming practices
* Changes to the phosphorus application period and nutrient allowance, with phosphorus incorporated into the soil at or before sowing of winter cereals.
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