This follows a four-year investigation into the club's finances by the Premier League.
The breaches are alleged to have taken place between the 2009/2010 and 2017/2018 seasons.
In 2020 Man City were handed a two-year ban by UEFA from European competitions for falling foul of financial fair play regulations.
The ban was later overturned by the Court of Arbitration for Sport(CAS) and the club have always denied any wrongdoing.
This latest charge has been referred to an independent commission and the club could face punishments ranging from points deduction, fines and expulsion from the Premier League.
In a statement, the Premier League said: “In accordance with Premier League rule W.82.1, the Premier League confirms that it has today [February 6 2023] referred a number of alleged breaches of the Premier League rules by Manchester City Football Club to a commission under Premier League rule W.3.4.
“Commissions are independent of the Premier League and member clubs. The members of the commission will be appointed by the independent chair of the Premier League judicial panel, in accordance with Premier League rules W.19, W.20 and W.26.
“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.”
