Farmers have been left "fully exposed to the additional costs generated" by the Carbon Border Adjustment Mechanism (CBAM), according to Copa Cogeca.
The umbrella organisation representing EU farmers and agri-cooperatives said the European Parliament's Committee on the Environment, Climate and Food Safety (ENVI) has removed the "only crisis safety valve for farmers".
This week, ENVI adopted its report on the revision of the CBAM.
Copa Cogeca said that farmers and agri-cooperatives had "hoped that parliament would strengthen the proposal by ensuring greater resilience during periods of market disruption".
However, the committee "instead chose to delete the only provision that would have allowed for the temporary suspension of the CBAM on fertilisers in times of crisis - Article 27a".
"Copa and Cogeca deeply regret this decision," it said.
"At a time of growing geopolitical instability and highly volatile fertiliser markets, removing this safeguard sends the wrong signal to Europe's farmers.
"Recent years have clearly demonstrated that fertiliser markets are highly vulnerable to external shocks, with immediate consequences for production costs, farm viability and ultimately Europe's food security."
The decision leaves farmers "fully exposed to the additional costs generated by the CBAM, even in exceptional circumstances when fertiliser prices are already soaring".
"This is particularly alarming given that fertilisers remain among the largest input costs for European agriculture and, for many arable farmers, represent the single biggest production expense," Copa Cogeca said.
"Without the possibility of temporarily suspending the mechanism during severe market disruptions, the CBAM risks exacerbating crises instead of cushioning their impact.
"What makes this decision particularly disappointing is that balanced solutions were available."
Copa Cogeca said it would have been "entirely possible" to preserve the objectives of supporting the decarbonisation and competitiveness of the European fertiliser industry while introducing a targeted and temporary crisis safeguard for farmers.
"Such an approach would have strengthened the resilience of the entire agri-food chain without undermining the long-term objectives of the CBAM," the organisation said.
Copa Cogeca is calling on members of the European Parliament to "urgently rectify this decision during the forthcoming plenary vote".
"Parliament still can restore a credible and operational crisis safeguard that protects European farmers when they need it most, while preserving the EU's industrial ambitions," it said.
"Europe's farmers should not be left to bear the full cost of future market shocks without any emergency safety mechanism."