The protesters started at the Barclays Center in Brooklyn and crossed the Brooklyn Bridge to City Hall Park, where they were met by a large number of officers.
Video from Citizen App showed the chaotic scene outside City Hall.
Demonstrators blocked traffic, threw bottles and vandalized property, and police started making arrests. An NYPD captain who was among the injured officers was struck in the helmet with a bottle.
Police Commissioner Dermot Shea blasted the march and the protesters' actions.
"It certainly does not resemble a peaceful protest," he told NY1. "You are bringing bottles, you are bringing graffiti, you are spray painting our city. This is our city. You are spray painting to burn our city down. This isn't actions that are caused by police officers."
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Mayor Bill de Blasio said the proximity of the protests to City Hall "was a concern, especially after the recent events at the Capitol."
"The bottom line is a host of changes are happening right now at the NYPD," he said. "This discipline matrix, this revolutionizes discipline. Anyone interested should really read it carefully. This is the way we change the culture and the reality."
Authorities said 28 people were arrested, mostly charged with disorderly conduct, obstructing governmental administration, resisting arrest, and blocking the roadway.
None of the police officers suffered serious injuries, though police are still looking for the suspect who hit the captain with the bottle.
Six of the uniformed officers refused medical attention, including the captain, while five were treated and released at area hospitals with various minor injuries.
The NYPD said the arrests began when a female using an iPhone to record protestors in front of the Municipal Building at 1 Centre Street had protesters move in to harass her.
Officers who formed a circle to protect and remove her then had glass bottles thrown at them. Other officers used a public address system to give clear, audible directions for protesters to leave the roadway.
The event was called the Black Liberation March organized to commemorate Martin Luther King Day.
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