The Philadelphia water department announced it will stop using water tests that scientists have said could conceal dangerous levels of lead.

Such tests are intended to monitor for corrosion, and protect the public from lead that can leach into water from home plumbing. But scientists at the US Environmental Protection Agency (EPA) have warned for 10 years that Philadelphia’s testing protocols underestimate the amount of lead, thus potentially deeming dangerous water sources safe.

A Guardian investigation of large cities in the eastern US found that Philadelphia had some of the most outdated testing practices on the eastern seaboard, using three methods the EPA warned against. Pennsylvania, and Philadelphia in particular, has struggled with elevated blood lead levels in children.

For the past six months, the department faced intense pressure to change its testing methods from clean water activists and a class-action lawsuit that alleged water department testing protocols “temporarily hide” lead contamination and that the city does not test enough high-risk homes.

“It’s surely a move in the right direction,” said Tony Spagnoli, one of the organizers of a citizen-led campaign to test water in hundreds of homes, called Philly Unleaded Project. The testing will be conducted at cost in Virginia Tech’s laboratory, which is separately testing water quality for the city of Flint, Michigan.

“We felt that part of it was the pressure that was mounting from the media and the citizens, that what they were doing was not sufficient,” said Spagnoli. “And of course from the EPA, who told them they were not in compliance, but weren’t pressuring them to change necessarily.”

Water departments typically ask residents to collect samples from their home taps. In its announcement, Philadelphia said it would stop using two maligned methods in particular, both of which impact how a sample is collected.

The first method, known as “pre-flushing”, asks residents to run their tap for a few minutes before a six-hour, federally mandated period when water must sit in pipes.

Scientists have warned for years this method could reduce lead found in tests. In a letter to activists, the EPA’s head of drinking water warned as early as 2008 the method could go against the “intent” of the regulation. In February, when three officials in Flint were criminally charged with manipulating test results, pre-flushing was specifically cited as a manipulation method.

The second method asks testers to remove the small filter at the end of their faucet, called an aerator. The EPA warned all water utilities in a 2006 memo that the testing method could reduce lead found in water. The EPA issued the warning after a trio of experts, including the current head of Philadelphia’s water department laboratory, found a lead poisoning case was missed because the local water department removed aerators before testing water for lead.

Philadelphia, however, had refused to change these methods even after experts said the methods could distort tests.

Instead, after experts questioned the methods in a Guardian story, Philadelphia lobbied the EPA to continue using the test methods in a nine-page letter.

“The news media is not the appropriate venue for resolving such questions concerning the science of lead and home sampling,” Gary Burlingame, the head of Philadelphia water department’s lab, said in the March letter to the EPA.

Meanwhile, attorneys in a class action lawsuit accused the city of “rigging its lead testing procedures” and failing to warn residents about the dangers of increased lead exposure from construction projects.

In addition to changing its testing protocols, the city promised to test more homes with lead plumbing components.

Though the city is required to test 50 homes with lead plumbing, it fell short of that total in its last three testing cycles. The city’s water department serves 1.7 million people in the city and surrounding Bucks County.

Officials complained it was difficult to enroll people in the testing regime. Letters sent to residents to solicit volunteers, obtained by the Guardian, showed that the city failed to mention any adverse health impacts from lead in water.

Burlingame explained in an email to activists in 2014, also obtained by the Guardian, that the water department avoided doing so because “there has not yet been to our knowledge a really clear message from EPA and health experts on lead”.