The European Commission is ending the long-standing Dutch exemption allowing farmers to spread more manure on their fields than is permitted elsewhere in the EU.

Caretaker agriculture minister Femke Wiersma said on Tuesday the loss of the special position enjoyed by Dutch farmers was “very disappointing”. She said the phased withdrawal would have “a very large negative impact on farmers’ incomes and future prospects”.

The decision was confirmed in a letter sent on Monday evening by EU environment commissioner Jessika Roswall. She said concerns about water quality and manure policy in the Netherlands had played a role in the decision to end the exemption.

Dutch farmers have been sanctioned to breach EU rules for 20 years. The European limit is 170 kilos of nitrogen from animal manure per hectare, compared with up to 250 kilos under the Dutch exemption.

The Dutch intensive farming sector has already been struggling to deal with reductions in the amount of manure farmers are allowed to spread on their fields, because of the risk of nitrates leaching into the waterways and the high concentration of nitrogen.

Dairy farmers are expected to be hit hardest by the EU’s decision, as they make most use of the additional manure allowances.

Wiersma, a member of the pro-countryside BBB, had asked the European Commission in July to extend the exemption, but NOS sources said it had long been clear that the Netherlands was likely to lose its special position.

In April, Roswall warned that the Netherlands first needed to deliver concrete improvements in terms of restoring damaged natural environments and tackling nitrogen-based pollution before any extension could be considered.

The loss of the exemption adds to a difficult end to the year for Wiersma. Earlier this week, the Council of State slammed the cabinet’s proposals to cut nitrogen emissions and parliament has also passed a motion preventing the minister from pursuing her own manure strategy.