Because the E.P.A. does not regulate the testing of water in schools, its guidance on pre-stagnation flushing does not apply directly to New York’s procedures. But the agency’s voluntary guidelines for schools do not recommend such flushing and generally direct schools to mimic normal consumption patterns when taking samples.

“The results should be thrown into the garbage, and the city should start over,” said Marc Edwards, a civil engineering professor at Virginia Tech who helped uncover dangerously high lead levels in the water in Flint, Mich., touching off scrutiny of drinking water across the country.

Yanna Lambrinidou, an anthropologist who has worked with Dr. Edwards to expose lead contamination in water in Washington, D.C., and elsewhere, and an affiliate faculty member at Virginia Tech’s Department of Science and Technology in Society, said in an email that New York City’s schools “may have just broken the national record for flawed testing.”

“Flushing is inappropriate any time you want to assess lead concentrations coming out of individual taps,” Dr. Lambrinidou wrote in the email. She said that water in schools is often stagnant for long periods of time — after school hours and on weekends, holidays and other breaks — and that the idea is to test it under conditions similar to those in effect when children might drink it. “Unless N.Y.C. schools flush every drinking water tap every evening for 2 hours routinely, their sampling technique is both unreliable and scientifically and morally indefensible,” she wrote.

Dan Kass, a deputy commissioner in the city’s Department of Health and Mental Hygiene, defended the process used to test the water. In an interview last week, he said the most important thing when sampling for lead was to have a period of stagnation, and that whether the water was flushed before that period began, and for how long, would not affect the results.