La’Ron Singletary, the city’s police chief, is among those retiring, as is Deputy Chief Joseph M Morabito – and possibly other senior commanders, Mayor Lovely Warren said.
Ms Warren made the surprise announcement of the retirements at a City Council briefing being held online.
Council members had expected the chief to appear in person to discuss ongoing protests over the death of Mr Prude, a 41-year-old black man who died several days after an encounter with police on March 23.
“As you all know, this has been a very challenging time for the city of Rochester, and the chief was not asked to give his resignation because I do believe that he’s giving his very best,” Ms Warren told council members.
In an emailed statement, Mr Singletary said that “the events over the past week are an attempt to destroy my character and integrity”.
“The members of the Rochester Police Department and the Greater Rochester Community know my reputation and know what I stand for,” he said in the statement.
“The mischaracterisation and the politicisation of the actions that I took after being informed of Mr Prude’s death is not based on facts, and is not what I stand for.”
Mr Singletary, who spent his entire career inside the Rochester Police Department, was appointed chief in April 2019. He said he looks forward to “continuing to serve our community in my next chapter”.
“This is great news,” said Iman Abid, speaking for Free the People ROC, which has held nightly protests since details of Mr Prude’s death emerged.
“It says to the people that people are able to move things and to shape things. The police chief wouldn’t retire if it weren’t for something that he felt he was accountable to.”
But, she said, nightly protests will continue to push other demands, including the resignation of the mayor, defunding and demilitarising of police, and development of a state law barring police departments from responding to mental health crises.
Ms Warren did not know when the retirements would take effect. It was unclear who would be in charge of police on Tuesday night if demonstrators come out for a sixth straight night, as expected. Demonstrators have called for the resignations of both Mr Singletary and Ms Warren, who are both black.
Officers found Mr Prude running naked down the street put a hood over his head to stop him from spitting, then held him down for about two minutes until he stopped breathing.
He died a week later after he was taken off life support.
His brother, Joe Prude, had called 911 seeking help for Daniel Prude’s unusual behaviour. He had been taken to a hospital for a mental health evaluation earlier that night but was released after a few hours, his brother told officers.
His death sparked outrage after his relatives last week released police body camera video and written reports they obtained through a public records request.
Seven police officers were suspended a day later, and state Attorney General Letitia James said she would form a grand jury and conduct an “exhaustive investigation” into Mr Prude’s death.
Police union officials have said the officers were following their training.