The mayor of Rochester, N.Y., was charged with two felonies on Friday over allegations of campaign-finance fraud, dealing another blow to an administration that has been rocked by the police-involved asphyxiation death of Daniel Prude.

Mayor Lovely Warren is accused of unlawfully coordinating the activities of her re-election campaign committee and an outside political-action committee while running for a second term in 2017, Monroe County prosecutors say.

The Democratic mayor as well as the treasurers of both political committees were charged with engaging in a scheme to defraud and violate the state’s campaign finance law. Monroe County District Attorney Sandra Doorley said the case arose from an investigation by the state Board of Elections enforcement counsel, which looked into a complaint by Ms. Warren’s political rivals.

Ms. Warren has repeatedly denied wrongdoing. Her attorney, Joseph Damelio, said at an afternoon news conference that it was possible mistakes were made but that there was no criminal intent, and the mayor didn’t intend to circumvent state election law.

Ms. Warren is scheduled for arraignment on Monday. If convicted of a felony, she could be removed from office.

The charges come after a series of tumultuous weeks in Rochester, the state’s third-largest city. Thousands of people have protested the March death of Mr. Prude, a Black man who died after he was restrained by Rochester Police Department officers responding to reports of a person acting erratically. Police placed Mr. Prude, who had a history of mental illness, in a spit hood and held him on the ground. He died seven days later in a hospital, and his death was ruled a homicide.

The circumstances surrounding Mr. Prude’s death only became public when his family held a Sept. 2 press conference and released police body-camera footage of his arrest. Ms. Warren said on Sept.