The EPA chief, Scott Pruitt, has ignored the scientific recommendation of his own agency to allow continued use of chlorpyrifos, despite its links to brain damage

Environmental groups have filed a complaint against the US government over its support of a pesticide linked to brain damage in children, one week after Donald Trump’s administration rejected federally backed science and reversed an Obama-era policy.

The Pesticide Action Network and the Natural Resources Defense Council (NRDC) filed the case against the US Environmental Protection Agency (EPA) on Wednesday, seeking to force the government to follow through with the Obama administration’s recommendations to ban an insecticide widely used in agriculture.

The appeal in San Francisco federal court sets the stage for one of the first major legal battles between the new EPA chief, Scott Pruitt, and environmental organizations. The case is centered on a pesticide called chlorpyrifos that researchers have concluded is correlated with lower IQ, attention deficit disorders and developmental delays.

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The chemical is a type of insecticide currently used on corn, strawberries, wheat, citrus, apples, broccoli and a number of other crops, as well as golf courses, turf and in greenhouses. Researchers and environmentalists have long fought for a full agricultural ban on the neurotoxic pesticide after the US government blocked the chemical for residential use in 2000 due to health concerns.

After years of litigation, the EPA released an assessment of chlorpyrifos in November, concluding that current usage of the pesticide carries dietary and drinking water risks. The EPA further concluded that the residues on food crops exceed safety standards and that there were risks to workers who apply chlorpyrifos to crops. The agency also raised concerns about risks associated with drift to schools and homes.

As a result of this growing body of research – including long-term studies suggesting moderate exposure during pregnancy can lead to long-term brain impacts on children – the Obama administration proposed banning all applications of chlorpyrifos on food.

Despite conclusions by experts in his agency, Pruitt reversed the move to ban chlorpyrifos last week, just before a federal court deadline to make a final decision on the pesticide. “We are returning to using sound science in decision-making,” he said in a statement.

The action from Pruitt, who has vowed to roll back climate change and pollution regulations, means the EPA will not have to re-evaluate potential health risks of chlorpyrifos until 2022.

“Given the science, we thought it seemed practically impossible to not move forward with the ban,” said Paul Towers, organizing director and policy advocate with the Pesticide Action Network. “We know it can have a profound impact on children’s brain architecture and their lifelong learning.”

The new complaint, filed by lawyers with advocacy group Earthjustice, asks a panel of three federal appeals court judges to order the EPA to permanently ban chlorpyrifos based on its own science.

Dow Chemical, which manufactures the pesticide under the name Lorsban, has aggressively lobbied to keep the product in use and claimed that the science is not conclusive. A spokesperson said in an email on Wednesday morning that the company is aware of the complaint, but has “not had sufficient time to review it”.

EPA representatives declined to comment.

Irva Hertz-Picciotto, a University of California, Davis environmental health sciences professor, compared chlorpyrifos to lead, which was widely used in the US until researchers proved that low-level exposures were harming children.

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“They used the term ‘silent epidemic’ with lead, and I think that’s really what we’re talking about here,” said Hertz-Picciotto, whose research has found links between autism and maternal exposure to the class of pesticides that includes chlorpyrifos. “The longer this goes on, the more accumulated evidence there is. It’s not like there is other evidence coming in that detracts from the conclusion that this is not safe and it’s not healthy.”

Research has further linked chlorpyrifos exposure to loss of working memory, delayed motor development and decreases in cognitive functioning.

“Parents shouldn’t have to worry that a dangerous chemical might be lurking in the fruits and veggies they feed their kids,” Miriam Rotkin-Ellman, senior scientist at NRDC, said in a statement.

“It’s eating away at the development of vulnerable brains,” added Hertz-Picciotto, who said she had hoped the ban initiated under Obama would have paved the way for further restrictions of harmful pesticides. “All bets are off at this point.”

Bonnie Wirtz, a farmer in Minnesota who said she was exposed to a chlorpyrifos drift from an alfalfa field when she was at her home, slammed Pruitt’s decision.

“By leaving this chemical on the market we are gambling with the lives of children and their long-term wellbeing and they have no choice in the matter,” she said in a statement. “That’s reckless and heartbreaking.”