The Trump administration issued an environmental notice of violation to San Francisco on Wednesday, fulfilling Donald Trump’s threat to cite the city over an inaccurate claim that linked water pollution with the city’s homeless crisis.

Trump said the Environmental Protection Agency (EPA) would issue a notice because the city allowed needles and waste from its homeless population to flow from the sewer system into the ocean – an allegation city officials disputed. In a letter Wednesday, the EPA administrator, Andrew Wheeler, accused the city of improperly discharging waste into the bay, but avoided mentioning Trump’s comments directly.

The letter states that the city’s incomplete data shows “it discharging approximately one and a half billion gallons of combined sewage annually onto beaches and other sensitive areas, including areas where recreation takes place”.

“The failure to properly operate and maintain the city’s sewage collection and treatment facilities” caused force main and pump station failures “that have diverted substantial volumes of raw and partially-treated sewage to flow across beaches and into the San Francisco Bay and the Pacific Ocean”, the letter states.

The notice of violation comes after the EPA sent a letter to the California governor, Gavin Newsom, accusing the state of failing to stop water pollution from human waste left by the homeless in cities like Los Angeles and San Francisco. The week before that, the Trump administration moved to revoke California’s authority to set automobile emission standards tougher than the federal government’s.

In a letter to Wheeler regarding his letter to Newsom, San Francisco public utilities commission general manager Harlan Kelly said the EPA’s allegation of “one billion gallons of combined sewage” dumped into the bay and ocean is mischaracterized.

“All combined sewer overflows are subject to equivalent-to-primary treatment before discharge,” Kelly wrote. “The frequency and volume of combined sewer overflows is consistent with the expected performance of the city’s combined sewer system and has been specifically authorized — for decades — by permits either issued jointly by EPA and California or by permits that have received EPA’s concurrence.”

San Francisco officials have repeatedly said that needles and human waste are not flowing into the ocean en masse. According to the city’s Public Utilities Commission, catch basins trap any debris coming out of storm drains, while two city treatment facilities process any runoff or pollutants that hadn’t been filtered out.

The city attorney Dennis Herrera responded to Wednesday’s notice by submitting a Freedom of Information Act request to the EPA “for records related to these unwarranted attacks on San Francisco”.

“These attacks on San Francisco are a politically motivated ploy,” Herrera said in a statement. “The Trump administration is ignoring facts and misusing the EPA to attack people it disagrees with.”

The city’s mayor, London Breed says the violation notice contains “mischaracterizations, inaccuracies and falsehoods” and says the city’s sewer system is one of the most effective in the country.

The move is the latest escalation in an ongoing feud between the progressive state and the Trump administration. The state attorney general, Xavier Becerra, has filed more than 60 lawsuits against the White House over issues ranging from immigration to the environment.

Agencies contributed reporting.