Advocacy organizations seeking to ban a pesticide linked to developmental disorders in children asked the courts Wednesday to intervene and order the Environmental Protection Agency to ban the pesticide from food within 30 days and from all uses within 60 days if it cannot prove it is safe.

The head of the E.P.A., Scott Pruitt, last week denied the petition to outlaw chlorpyrifos, a pesticide often used on apples, oranges and other crops, even though the agency’s own safety experts concluded that the chemical should be outlawed. Mr. Pruitt did not present any new evidence that it is safe.

The E.P.A. had been under a court order to respond by the end of March to a 10-year-old petition to ban the chemical, originally filed in 2007 by the Natural Resources Defense Council and Pesticide Action Network.

The most recent E.P.A. analysis concluded that children were being exposed to up to 140 times the safe levels of the pesticide through food alone. An earlier report said drinking water can also be contaminated.

“The science is clear that this chemical is dangerous,” said Erik Olson, senior attorney and director of the health program at N.R.D.C. “We are asking the court to step in to keep our children safe.”

An E.P.A. report issued last November concluded the risks justified a complete ban on chlorpyrifos, citing studies on pregnant women and children done at Columbia University that found evidence of neurodevelopmental effects in children whose mothers were exposed to chlorpyrifos in pregnancy. Dow Chemical, which makes the product, has argued that the science is inconclusive. An expert review panel of scientists also raised questions about the methodology the agency had used, leading to revisions but not altering the recommendation for a ban.

Earthjustice, a public interest law group that represents N.R.D.C. and P.A.N., filed the motion to enforce the previous court order in the Ninth Circuit Court of Appeals in San Francisco. The E.P.A. declined to comment, a spokesman said.

Chlorpyrifos is one of the most widely used pesticides in the world and, in terms of pounds of active ingredient, the most widely used conventional insecticide in the United States. It is typically sprayed on apples, oranges, strawberries, broccoli, cauliflower, almonds, walnuts, cherries, peaches, pears, corn and wheat.

The chemical was once the main active ingredient in household pesticide products like Raid, but indoor use of chlorpyrifos was phased out starting in 2000 because of potential health concerns. Indoor use is now permitted only in child-resistant ant and roach baits.

It can still also be used on golf courses and in greenhouses and for public mosquito control efforts.

Under the 1996 Food Quality Protection Act, which changed the way pesticides used on foods are regulated, the E.P.A. is required to make sure a pesticide can be used with “a reasonable certainty of no harm.” The act mandated the agency take the unique vulnerabilities of infants and children into consideration as well.

Several members of Congress have also expressed dismay at Mr. Pruitt’s decision. In a letter to Mr. Pruitt, Senator Thomas R. Carper, Democrat of Delaware and a ranking member of the Committee on Environment and Public Works, said he was “troubled” by the E.P.A.’s reversal on chlorpyrifos, absent “any new scientific analysis to support this decision.”

“The previous finding to ban chlorpyrifos was based on extensive data, models and research developed by industry, government and academic scientists,” Senator Carper wrote in his March 31 letter. “Absent such justification, this decision to lift the proposed ban could undermine the trust the public has in the agency to keep its food, water and air safe.”

Representatives Frank Pallone Jr. of New Jersey, Gene Green of Texas, Diana DeGette of Colorado and Paul D. Tonko of New York, all Democrats, signed a letter saying they were concerned that the Trump administration is not implementing the Food Quality Protection Act. They urged Representative Greg Walden, Republican of Oregon and the chairman of the Energy and Commerce Committee, to start an investigation.

They noted that the E.P.A. also recently expanded the use of another controversial chemical used in agriculture, glyphosate, the main ingredient in Roundup weed killer, and raised concerns about the possibility of political meddling in decisions, specifically asking whether “trade associations representing the Trump Organization golf courses or lobbyists who represent the Trump Organization” pressured the E.P.A. to drop the proposed chlorpyrifos ban.