“Our own observations and other technical advice we have received have identified a number of significant challenges to the long-term goal of reliable and sustainable clean drinking water for the city of Flint,” McCarthy wrote in a letter dated Thursday and posted on the agency’s website. “These challenges go well beyond the immediate crisis problems we have all been working so hard to address.”

For instance, McCarthy said that Flint’s water-treatment plant is “not adequately staffed, operated or administered to reliably deliver safe drinking water for years into the future.” She cited a report that found the system would need additional experienced employees and a more-reliable maintenance and training program to function reliably in the years ahead.

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McCarthy wrote that Flint’s water-distribution system is too large for both the current and the projected water demand in the city. That could hamper the ability to provide reliably clean water, because oversize water-distribution systems — Flint’s was built when the city had a significantly larger population — can result in water not flowing properly through pipes, opening the door to the growth of potentially harmful pathogens.

Thursday’s letter also said the city’s leaders must provide the “stable, reliable and quick” support necessary to operate a functioning water system. That includes the ability to rapidly hire or contract for necessary maintenance or technical support. Of course, ensuring that will take financial resources, which are sorely lacking in Flint.

“City residents already pay one of the highest water rates in the nation, and all of the necessary actions to ensure safe drinking water will require additional investments,” McCarthy wrote. “As the state and city plan for the long-term future, a solid and realistic financial plan will be essential.”

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Neither the Flint mayor’s office nor a spokesman for Snyder responded immediately to a request for comment. However, a spokeswoman for the governor told the Flint Journal that McCarthy’s letter is being reviewed “so we can work with the city to address the issues raised.”

“Both the city and the state are aware of the challenges that need to be resolved and are making steady progress toward solutions,” the spokeswoman said in an email.

In an emailed statement, Flint Mayor Karen Weaver said that McCarthy’s letter “confirms a lot of what we’ve been saying in Flint for months, if not longer. We not only need new pipes, we need new infrastructure.”

Weaver said that the city is wrestling as best it can with the issue of having sufficient staff, given that its finances had been under the control of a state-appointed emergency manager whose cost-cutting measures included reducing staff at the water plant. She said the city needs more outside support to ensure safe drinking water for citizens in the coming months and years.

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“Flint city officials recognize the challenges and possibilities identified by the EPA. The fact that EPA has been in Flint since January yet only took action to identify the systems needed in late May attest to the fact that all government organizations, large and small, have shortcomings,” Weaver said. “This water crisis and the resources needed to fix it are much bigger than the City of Flint. We did not create this mess, and the burden to make things right should not be ours alone.”

The lead problems in Flint’s water surfaced after the city temporarily switched to the Flint River for its water supply beginning in April 2014, as part of a budget-cutting move. State regulators failed to ensure that anti-corrosion chemicals were added to the water, which was contaminated when lead leached into it from aging underground pipes.

As a result, officials say, nearly 9,000 children ages 6 and younger have been exposed to the toxic contaminant. Lead can cause permanent learning disabilities, behavioral problems and, at higher levels, a number of diseases. Public health officials say there is no safe level of lead in the body.

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In April, researchers from Virginia Tech University said Flint’s water system is in far better shape since the city switched its water source in the fall and began adding chemicals to control the corrosion of aging pipes. But they made it clear that the threat of lead contamination remains.

“The system is definitely on its path to recovery,” Marc Edwards, the Virginia Tech professor whose work helped bring Flint’s water crisis to light, said at the time. But because recent samples showed that potentially dangerous levels of lead persist, “at present, no one should be drinking unfiltered water in Flint.”

Authorities have said it will take months before they deem the water safe to drink again.

This post has been updated.