The breaches stretch from the 2009/10 season to the 2017/18 campaign, the league added. City were acquired by their Abu Dhabi-based owners, City Football Group, in 2008.
If the charges are proved City, could face a range of sanctions, including a points deduction or expulsion from the Premier League.
City are alleged to have breached rules relating to the provision of accurate financial information, "in particular with respect to its revenue (including sponsorship revenue), its related parties and its operating costs," the league said.
The charges stem from a Premier League investigation into City's financial dealings launched four years ago, months after the release of a tranche of 'Football Leaks' documents obtained by the German publication Der Spiegel and reviewed by Reuters.
City were subsequently banned from the Champions League by European governing body UEFA for two years, but successfully appealed to the Court of Arbitration for Sport (CAS), which overturned the ban in 2020.
The club were fined 30 million euros by UEFA, which CAS reduced to 10 million euros.
City are alleged by the Premier League to have not fully disclosed managerial remuneration in each of the seasons from 2009/10 to 2012/13 when Roberto Mancini (58) was manager.
City are also charged with failing to comply with Premier League's rules requiring clubs to follow UEFA's financial fair play regulations from the 2013/14 to 2017/18 seasons and failing to follow the Premier League's rules on profit and sustainability from the 2015/16 to 2017/18 seasons.
"The members of the Commission will be appointed by the independent Chair of the Premier League Judicial Panel," the Premier League said in a statement.
"The proceedings before the Commission will... be confidential and heard in private.
"The Premier League will be making no further comment in respect of this matter until further notice."
Club statement
Manchester City have responded by announcing they are, "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," they added in their official statement.