The European Parliament voted against a list produced by the European Commission of criteria to help identify what are known as endocrine disruptors in products used to protect farm animals and plants from disease and insects.
Endocrine disruptors are believed to have a role in many health conditions, from obesity to infertility, and are found in many common goods such as cosmetics or even toys.
"Parliament blocked an EU Commission proposal which would have exempted some chemicals in pesticides from being identified as endocrine disruptors, on Wednesday," parliament said in a statement.
The setback came just three months after an apparent breakthrough in a three-year stand-off over the chemicals, when EU member states approved the commission's list.
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EU Health Commissioner Vytenis Andriukaitis said in a statement that he "regrets" the parliament decision, adding that "in this case no deal is a bad deal for EU citizens."
"The commission will now need to reflect on next steps to take," he said.
The body's endocrine system -- in the ovaries and testes, as well as the adrenal, pituitary and thyroid glands -- produce hormones that are secreted into the bloodstream to control and coordinate a range of critical body functions.
The disruptors issue has pitted industry and agriculture against consumer and environmental groups for many years.
The EU even announced last year that it had reached broad agreement on what substances were involved but had to go back to the drawing board amid controversy.