The 27-year-old, who joined the club in 2017, is on six year deal with the club worth a reported $53m. Man City also paid a $98m transfer fee to sign Mendy from Monaco.
"Manchester City can confirm that following his being charged by police today, Benjamin Mendy has been suspended pending an investigation," the club said in a statement.
"The matter is subject to a legal process and the club is therefore unable to make further comment until that process is complete."
The charges relate to incidents that allegedly occurred between October 2020 and August this year.
In a statement, police said Mendy would remain in custody overnight, before appearing in court on Friday.
"The Crown Prosecution Service (CPS) has authorised Cheshire Constabulary to charge a man in connection with allegations of sexual assault," the statement says.
"Benjamin Mendy, aged 27, has been charged with four counts of rape and one count of sexual assault.
"The charges relate to three complainants over the age of 16 and are alleged to have taken place between October 2020 and August 2021.
"Mendy has been remanded in police custody and is set to appear at Chester Magistrates' Court on Friday 27 August.
"Cheshire Constabulary and the Crown Prosecution Service would like to remind everyone that criminal proceedings against Mendy are live and that he has a right to a fair trial."
Mendy was a member of the French squad that won the 2018 World Cup.
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