A peaceful march was led by the Black Visions Collective from Bottineau Park in the city with chants of “Black Lives Matter” and “Defund the police, give the money to the community”, CBS affiliate WCCO reports.
Protesters made it clear that they were not just interested in defunding the police department but abolishing it.
Mayor Frey was seen in the crowd and invited up front to speak and asked directly by a protest organiser if he would commit to defunding the police department.
It was pointed out that his re-election bid in 2021 would hinge on his answer.
The mayor refused to commit and was drowned out by the crowd which erupted in boos and chanted “Go home, Jacob, go home,” and “shame”. Videos from the scene showed the mayor walking solemnly through the crowd with his head bowed.
The mayor, a former civil rights attorney, took office two years ago vowing to repair the police department's strained relations with minorities.
Mr Frey has decried the deadly use of force in Mr Floyd's 25 May arrest as unjustified.
As street protests raged amid incidents of arson and looting that went largely unchecked by police, Mr Frey drew criticism from some, including Donald Trump, for doing too little to restore order. He ultimately imposed a curfew to help quell the disturbances.
Many protesters have called for defunding and dismantling the police department altogether, and instead shifting city dollars into public health programmes and other initiatives aimed at preventing violent crime.
WCCO caught up afterwards with Mr Frey, who told the television station that he favoured “massive structural reform to revise a structurally racist system".
He added: “I'm not for abolishing the entire police department. I will be honest about that.”
A spokesperson for the mayor told CNN that the mayor is unwavering in his commitment to working with Minneapolis police chief Medaria Arradondo “toward deep structural reforms and uprooting systemic racism. He does not support abolishing the police department".
Democratic lawmakers in Washington are set to launch legislation on Monday that if passed would be the most ambitious overhaul of law enforcement in memory.
With reporting from Reuters
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