WASHINGTON — Scott Pruitt, the head of the Environmental Protection Agency, moved late on Wednesday to reject the scientific conclusion of the agency’s own chemical safety experts who under the Obama administration recommended that one of the nation’s most widely used insecticides be permanently banned at farms nationwide because of the harm it potentially causes children and farm workers.

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.