The controversial Action Programme, under the EU nitrates directive aimed at protecting the quality of groundwater in Ireland, came into force at midnight yesterday.
The Irish Farmers Association immediately called on Minister for the Environment Dick Roche to amend it or it could not support a new partnership agreement.
"Partnership is a two-way street and the Government was introducing highly damaging legislation that would do nothing to improve water quality, which is the objective of the directive," said IFA president Padraig Walshe.
Mr Walshe said the regulations were unworkable and damaging to all farmers, including the 50,000 of them who participate in the Rural Environment Protection Scheme (Reps).
Last night, however, Minister for Agriculture and Food Mary Coughlan said that because of the short deferral of the phosphate part of the regulation, farmers in Reps could carry on as they were for the time being.
"Until such time as part three of the regulations is implemented, farmers in Reps can continue to operate under the terms of their existing contracts as far as nutrient management is concerned.
"For Reps planning, too, the existing specifications remain in force," the Minister said.
Last night a Department of Agriculture spokesman said this would also apply to farmers who had prepared plans for entry into the Reps scheme.
The nitrates directive limits the use of livestock manure on farms to 170kg per hectare and also limits the usage of phosphorus.
There are mandatory storage periods from 16 weeks in east coast farms, 18 weeks in most of the western counties, 20 weeks in Donegal and Leitrim and 22 weeks in Cavan and Monaghan.
There are prohibitions on spreading fertiliser in most of the winter months, and pig and poultry farms must have storage facilities for 26 weeks, unless there is sufficient land for spreading.
There are limits on the spreading of soiled water, and chemical fertilisers cannot be applied on land within 1.5m of a surface watercourse.
Organic fertiliser or soiled water cannot be applied within 200m of areas where water is being extracted for human consumption.
A regulation causing great difficulty to farmers in hilly areas states that no fertiliser or soiled water can be applied within 10m where the land would have an average incline greater than 10 per cent towards any surface watercourse.
