The move from the Republican president came as he tries to bolster the “law and order” image he hopes will win him re-election in November.
Earlier in September Trump requested the Department of Justice identify municipal governments “permitting anarchy, violence, and destruction in American cities.”
In recent months anti-racism protests have mushroomed nationwide in response to police violence that disproportionately harms black people.
On Monday the Department of Justice accused the city governments of New York, Portland and Seattle of failing to control their populations, citing a spike in shootings, protests and looting.
It also noted that New York had reduced its police budget, facing increasing public pressure to use government money for health, education and mental health resources.
The DOJ notably did not single out sometimes violent protests in cities in Minnesota and Wisconsin -- key states in November’s vote -- despite prolonged demonstrations against police brutality there.
“When state and local leaders impede their own law enforcement officers and agencies from doing their jobs, it endangers innocent citizens who deserve to be protected, including those who are trying to peacefully assemble and protest,” said Attorney General Bill Barr in a statement announcing the designations.
“It is my hope that the cities identified by the Department of Justice today will reverse course and become serious about performing the basic function of government and start protecting their own citizens.”
New York City mayor Bill de Blasio dismissed the move as “another one of President Trump’s games.”
“It’s not based in the fact in the least,” the Democratic leader of the already cash-strapped city said. “It’s insulting to the people of New York City.”
“His effort to withhold our funding is unconstitutional.”
Federal efforts to withdraw money from the cities on the list will likely get tied up in the courts.
“The president does not have the authority to change the will of Congress,” said James Johnson, New York’s chief city lawyer.
“We are preparing to fight this in court if... he actually takes concrete steps to withdraw federal funds.”