A day after the title hopes were dented by Tottenham Hotspur, City face points deduction or relegation due to their alleged over expenditure.
This is after the Premier League charged the club with more than 100 breaches of its financial rules following a four-year investigation.
It has referred the club to an independent commission over alleged rule breaches between 2009 and 2018.
It also accused City of not co-operating since the investigation started in December 2018.
City said they were “surprised” by the charges and are supported by a “body of irrefutable evidence”.
The commission can impose punishments ranging from a fine and points deduction to expulsion from the Premier League.
“Manchester City is surprised by the issuing of these alleged breaches of the Premier League Rules, particularly given the extensive engagement and vast amount of detailed materials that the EPL has been provided with,” the club said in a statement.
“The club welcomes the review of this matter by an independent commission, to impartially consider the comprehensive body of irrefutable evidence that exists in support of its position.
In 2020 European football governing body Uefa ruled that City committed “serious breaches” of FFP regulations between 2012 and 2016.
However, a two-year ban from European competitions was overturned by the Court of Arbitration for Sport (Cas) later that year.
Uefa began its investigation into City after German newspaper Der Spiegel published leaked documents in November 2018 alleging the club had inflated the value of a sponsorship deal.
Last season City won their sixth Premier League title since the 2008 takeover by the Abu Dhabi United Group.