The government had been preparing a third and final annual dispensation to cover the 2023 sugar beet crop.
Sugar beet growers group CGB condemned the "brutality of the decision" a few weeks before spring planting.
That could further discourage sugar beet growers who faced drought-related yield losses last year and put a question mark over sugar production capacity.
"When sugar manufacturers don't have enough sugar beet they have to close.
The EU court's ruling followed a challenge to a similar exemption for neonicotinoid use on sugar beet in Belgium.