Syngenta said in a statement on its website that the decision not to allow re-registration of atrazine and a sister product, simazine, was taken by the EU's Standing Committee on the Food Chain and Animal Health.
The 45 year-old herbicide, used to kill weeds around crops, has been implicated by authorities in incidents of ground water contamination, prompting recent bans on its use in several European countries including France.
Exposure to excessive amounts of atrazine can potentially cause heart, lung and kidney trouble as well as cancer, according to the US Environmental Protection Agency.
Commenting on the EU regulator's move, Syngenta said it "regrets this decision as it overrides the science-based process for product registration".
"A favorable EU science review demonstrated the safety of the products to humans and the environment as part of the EU registration process," it added.
Syngenta said it was already offering alternatives to the herbicide in Germany and Italy, and would extend them to the rest of the EU.