The ruling by Mr. Pruitt, in one of his first formal actions as the nation’s top environmental official, rejected a petition filed a decade ago by two environmental groups that had asked that the agency ban all uses of chlorpyrifos. The chemical was banned in 2000 for use in most household settings, but still today is used at about 40,000 farms on about 50 different types of crops, ranging from almonds to apples.

Late last year, and based in part on research conducted at Columbia University, E.P.A. scientists concluded that exposure to the chemical that has been in use since 1965 was potentially causing significant health consequences. They included learning and memory declines, particularly among farm workers and young children who may be exposed through drinking water and other sources.

But Dow Chemical, which sells the product under the trade name Lorsban, along with farm groups that use it, had argued that the science demonstrating that chlorpyrifos caused such harm is inconclusive — especially when properly used to kill crop-spoiling insects.

An E.P.A. scientific review panel made up of academic experts last July also had raised questions about some of the conclusions the chemical safety staff had reached. That led the staff to revise the way it had justified its findings of harm, although the agency employees as of late last year still concluded that the chemical should be banned.

Mr. Pruitt, in an announcement issued Wednesday night, said the agency needed to study the science more.

“We need to provide regulatory certainty to the thousands of American farms that rely on chlorpyrifos, while still protecting human health and the environment,” Mr. Pruitt said in his statement. “By reversing the previous administration’s steps to ban one of the most widely used pesticides in the world, we are returning to using sound science in decision-making — rather than predetermined results.”

The United States Department of Agriculture, which works close with the nation’s farmers, supported Mr. Pruitt’s action.

“It means that this important pest management tool will remain available to growers, helping to ensure an abundant and affordable food supply for this nation,” Sheryl Kunickis, director of the U.S.D.A. Office of Pest Management Policy, said in a statement Wednesday.

Dow Agrosciences, the division that sells the product, also praised the ruling, calling it in a statement “the right decision for farmers who, in about 100 countries, rely on the effectiveness of chlorpyrifos to protect more than 50 crops.”

But Jim Jones, who ran the chemical safety unit at the E.P.A. for five years, and spent more than 20 years working there until he left the agency in January when President Trump took office, said he was disappointed by Mr. Pruitt’s action.

“They are ignoring the science that is pretty solid,” Mr. Jones said, adding that he believed the ruling would put farm workers and exposed children at unnecessary risk.

The ruling is, in some ways, more consequential than the higher profile move by Mr. Trump on Tuesday to order the start of rolling back Obama administration rules related to coal-burning power plants and climate change.

In rejecting the pesticide ban, Mr. Pruitt took what is known as a “final agency action” on the question of the safety and use of chlorpyrifos, suggesting that the matter would not likely be revisited until 2022, the next time the E.P.A. is formally required to re-evaluate the safety of the pesticide.

Mr. Pruitt’s move was immediately condemned by environmental groups, which said it showed that the Trump administration cared more about catering to the demands of major corporate players, like Dow Chemical, than the health and safety of families nationwide.

“We have a law that requires the E.P.A. to ban pesticides that it cannot determine are safe, and the E.P.A. has repeatedly said this pesticide is not safe,” said Patti Goldman, managing attorney at Earthjustice, a San Francisco-based environmental group that serves as the legal team for the Natural Resources Defense Council and the Pesticide Action Network of North America, which filed the petition in 2007 to ban the product.

The agency had been under court order to issue a ruling on the petition by Friday. The environmental groups intend to return to the Ninth Circuit Court of Appeals in San Francisco to ask judges to order the agency to “take action to protect children from this pesticide” Ms. Goldman said on Wednesday.

Scott Pruitt, the head of the Environmental Protection Agency, on Tuesday. Mr. Pruitt rejected a petition filed a decade ago by two environmental groups asking that the agency ban all uses of chlorpyrifos.Credit Jim Watson/Agence France-Presse — Getty Images

Scott Pruitt, the head of the Environmental Protection Agency, on Tuesday. Mr. Pruitt rejected a petition filed a decade ago by two environmental groups asking that the agency ban all uses of chlorpyrifos.Credit Jim Watson/Agence France-Presse — Getty Images