The disaster in Flint, sparked when authorities failed to treat drinking water for lead, prompted criminal charges againstthree government employees: Mike Glasgow, Stephen Busch and Mike Prysby.

Marc Edwards, the scientist who first uncovered the crisis in Flint, described water testing in some of America’s largest cities as an “outrage”.

“They make lead in water low when collecting samples for EPA compliance, even as it poisons kids who drink the water,” Edwards, a Virginia Tech scientist, said. “Clearly, the cheating and lax enforcement are needlessly harming children all over the United States.

“If they cannot be trusted to protect little kids from lead in drinking water, what on Earth can they be trusted with? Who amongst us is safe?”

For 25 years, the Environmental Protection Agency has required water utilities to test a small pool of households for lead contamination at least every three years. Typically, city water departments ask residents to collect these water samples. But the way residents are instructed to sample their water, as well as which households are chosen for testing, can profoundly impact how much lead is detected.

Testing methods that can avoid detecting lead include asking testers to run faucets before the test period, known as “pre-flushing”; to remove faucet filters called “aerators”; and to slowly fill sample bottles. The EPA reiterated in February that these lead-reducing methods go against its guidelines, and the Flint charges show they may now be criminal acts.

The arrest warrant for Glasgow, Busch and Prysby states that the men “did properly manipulate the collection of water samples by directing residents to ‘pre-flush’ their taps by running the water for five minutes the night before drawing a water sample and/or did fail to collect required sampled included in the tier 1 category of service lines.”

The tactic of pre-flushing, which helps clear lead from home plumbing prior to a test, is rampant across many large cities. In their most recent test cycles, Philadelphia; Milwaukee, Wisconsin; and Buffalo, New York, tested water for lead in this way.

The EPA has warned since 2008 that pre-flushing is problematic and goes against the “intent” of regulations designed to detect lead. Nevertheless, the federal agency failed to properly police state agencies who included the method in sample instructions for years, including at the Maine and Rhode Island departments of health.

Further distortion is achieved through the removal of “aerators” – the small metal filters at the tip of faucets. These filters can collect lead particles and add to lead detected in tests. The EPA has warned against this practice since 2006, when it became clear that a lead poisoning case in Durham, North Carolina, was missed by the water department at least partly because it routinely removed the filters.

Philadelphia, a city accused of having the worst water testing in the US, asks testers to pre-flush their pipes, remove aerators and slowly pour water into a sample bottle. The EPA has warned against all these testing methods, which could “mask the added contribution of lead at the tap”.

Documents show some authorities have also removed high-risk homes from testing or sought to obscure their dangerous lead levels. In Michigan, a department of environmental quality (MDEQ) official told the director of a town water department in a Detroit suburb called Howell to “bump this one out”, referring to a sample with high lead levels, by taking additional samples.

“I would suggest at least five more samples,” Adam Rosenthal, an official at the MDEQ drinking water office wrote in an email in 2008.

New Hampshire offered similar advice to water system officials in that state, advising water departments to test early so any high results could be re-tested.