The US Environmental Protection Agency aims to “strengthen” existing safe water laws, in response to findings that many cities are downplaying the levels of lead in their water.

Since news proliferated of dangerous lead contamination in Flint’s water, the Guardian revealed that numerous US cities and states, including Philadelphia, Detroit and Rhode Island, advise residents to run their faucets for several minutes the night before taking a sample of water for lead tests.

The EPA, which has come under fire for its response to the Flint crisis and its reluctance to stamp out the altered tests, will work to clarify best practice with water authorities, a spokeswoman told the Guardian. An update to the 25-year-old lead and copper rule is expected in 2017 but the EPA said it would act in the meantime.

The EPA’s comments come as it is poised to face greater public scrutiny in a hearing before Congress Wednesday morning, over its administration of the Safe Drinking Water Act in Flint, Michigan. Acting deputy administrator Joel Beauvais and EPA researcher Miguel Del Toral will testify before the House Oversight committee, along with state and local officials.

Philadelphia, which also asks residents to remove the aerator from faucets prior to the test, has launched an investigation into its water testing practices following the toxic water crisis in Flint and the Guardian’s reporting.

While not illegal, the widespread modifications to water tests are contrary to EPA advice and have been shown by scientists to lower the lead content in samples.

An EPA spokeswoman said that the agency recently advised water authorities in Flint and also Michigan at large to “remove instructions for pre-stagnation flushing from their instructions to samplers”.

“In December 2015, the agency received extensive recommendations from its national drinking water advisory council and other concerned citizen groups, some of which discussed pre-stagnation flushing,” the spokeswoman said.

“But even as the agency considers revisions, it will continue to engage with state and water systems on potential nearer-term steps that could strengthen implementation of the existing rule.”

She added: “Removal and cleaning of the aerator is advisable on a regular basis. However, if customers are only encouraged to remove and clean aerators prior to drawing a sample to test for lead, the public water system could fail to identify the typically available contribution of lead from that tap, and thus fail to take additional actions needed to reduce exposure to lead in drinking water.

“Therefore, homeowners should not remove or clean aerators prior to or during the collection of tap samples for lead.”

The EPA has faced criticism over the loopholes in the lead and copper rule, with the head of the Ohio EPA warning that they risk causing serious public health problems akin to concerns in Flint, where a state of emergency has been declared after authorities failed to act over health problems experienced by residents for more than a year.

Water authorities are obligated to put out public warnings over lead in water if the lead content exceeds 15 parts per billion in water samples. However, the “pre-flushing” of faucets the night before water sampling tests can lower the lead content in samples and therefore understate lead contamination from corroded pipes.

Philadelphia is set to hold hearings into its water testing practices within the next month after a public health advocate warned that the city’s procedures are “worse than Flint”.

A spokeswoman for the Philadelphia water department said: “We are continuing to work with the EPA and the state department of environmental protection on the implementation of nearer-term steps that could strengthen implementation of the existing rule.”

Meanwhile, Detroit’s water and sewerage department said it has not been responsible for water testing since 1 January, when responsibilities were handed to the the Great Lakes water authority. However, the Great Lakes water authority said that the water and sewerage department was still responsible for tests.