“This result illustrates how pre-stagnation flushing can mask serious lead in water problems in schools,” Marc Edwards, a professor of civil and environmental engineering at Virginia Tech who helped uncover elevated lead levels in the water in Flint, Mich., said in an email. “I applaud their retesting in a manner that better reveals the widespread scope of the contamination and health concern.”

Although no level of exposure to lead is considered safe, Professor Edwards said that any tap providing water with a lead level of more than 400 parts per billion represented “an acute health risk” to young children.

Water absorbs lead when it sits stagnant in pipes for long periods of time. For that reason the E.P.A. recommends that schools testing for lead take samples after water has been sitting in pipes for at least eight hours.

In 2016, amid the water crisis in Flint, New York moved to test the water in its more than 1,500 school buildings. Older buildings often have pipes and fixtures that contain lead, and young children are particularly at risk from exposure to lead, which can harm the developing brain.

Under the protocol the city used for the initial tests, workers went into schools at night, turned on all outlets and let the water run for two hours. The outlets were then turned off, and the water sat in pipes overnight for eight hours before samples were taken. The E.P.A.’s guidelines for schools do not address this practice, but experts say it temporarily reduces lead levels because it cleans the inside of pipes of soluble lead.

After finishing the tests, the city announced that only 1 percent of the outlets in schools had been found to have lead concentrations above the E.P.A. action level, that those outlets had been removed and that the water was safe.

In September, after The New York Times reported on the city’s flushing practice, citing experts who said it could distort the test results, officials said the city would adjust its protocol and avoid pre-stagnation flushing in most cases.