The Premier League issued a statement on its website announcing the club - who have won the competition six times since 2011 - had been referred to an independent commission in respect of a series of alleged breaches of rules related to club finances.
The alleged breaches concerned the reporting of accurate financial information, the submission of details of manager and player pay information within the relevant contracts, a club's responsibility as a Premier League member to adhere to UEFA's Financial Fair Play regulations and to the league's own profitability and sustainability regulations.
The club are also alleged to have breached rules requiring them to co-operate and assist with the Premier League's investigation into those breaches, which the league says began in December 2018.
Manchester City issued a statement expressing surprise at the announcement of the alleged rule breaches, which referred to "extensive engagement" with the Premier League on the matter.
The club also said they held "irrefutable evidence" in support of their position.
Premier League rule W.51 covers the sanctioning powers available to commissions should alleged breaches of league rules be found proven.
These range from a reprimand, through the deduction of points up to a recommendation to the league to expel a club from the competition.
The commission has the power to make such sanctions conditional on defined actions being taken within a fixed time period, and respondents have a right of appeal.
City's statement said: "Manchester City FC 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 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.
"As such we look forward to this matter being put to rest once and for all."
The club's chief executive Ferran Soriano is understood to have only been notified by his Premier League counterpart Richard Masters of the referral over alleged breaches as the statement was going live on the league's website.
The club are also mindful of the timing of the Premier League flexing its regulatory muscle on financial matters, when a Government White Paper - set to include plans for an independent regulator - is close to being published.
City have previously vigorously fought and denied charges relating to alleged breaches of UEFA FFP rules. They were found guilty by UEFA's club financial control body's adjudicatory chamber of "serious breaches" of FFP rules in February 2020 and handed a two-year UEFA competition ban, but this sanction was overturned on appeal at the Court of Arbitration for Sport in July of the same year.
The chair of the independent Premier League judicial panel is Murray Rosen KC, who was appointed in 2020.
The chair will select individuals to sit alongside him on a commission to consider the alleged rule breaches in this case. The panel also has access to consult other independent financial and legal experts.
The alleged breaches span a period from the 2009-10 season to the 2017-18 campaign.
The club are alleged to have breached league rules requiring provision "in utmost good faith" of "accurate financial information that gives a true and fair view of the club's financial position".
The league says the accurate financial information required relates to "revenue (including sponsorship revenue), its related parties and its operating costs".
The second set of breaches listed refers to alleged breaking of rules "requiring a member club to include full details of manager remuneration in its relevant contracts with its manager" related to seasons 2009-10 to 2012-13 inclusive.
The club's manager between December 2009 and May 2013 was current Italy boss Roberto Mancini.
The second set of alleged breaches also refers to requirements for a club to include full details of player remuneration within the relevant contracts, for the seasons 2010-11 to 2015-16 inclusive.
The third section deals with alleged breaches of Premier League rules requiring clubs to comply with UEFA Financial Fair Play regulations, between 2013-14 to 2017-18.
The fourth set of alleged breaches relates to the Premier League's profitability and sustainability rules in seasons 2015-16 to 2017-18 inclusive.
Finally, the club are alleged to have breached league rules requiring member clubs to co-operate with and assist the Premier League with its investigations, from December 2018 to date.
The Premier League statement concluded: "The proceedings before the Commission will, in accordance with Premier League Rule W.82, be confidential and heard in private. Under Premier League Rule W.82.2, the Commission's final award will be published on the Premier League's website.
"This confirmation is made in accordance with Premier League Rule W.82.1. The Premier League will be making no further comment in respect of this matter until further notice."