City was alleged to have broken rules relating to FFP, third-party ownership and youth player recruitment in articles by German publication Der Spiegel, which drew upon documents purportedly obtained by whistleblower Football Leaks.
UEFA's Club Financial Control Body (CFCB) opened a probe into the club in March, with former Belgian Prime Minister Yves Leterme leading as chief investigator but City slammed the move, describing it as a "hostile process".
The Premier League champion has taken its appeal against the investigation to CAS, the organisation confirmed in a statement.
"The appeal is filed against decisions taken by the Investigatory Chamber (IC) of the UEFA Club Financial Control Body (CFCB) regarding MCFC's alleged non-compliance with UEFA's Club Licensing and Financial Fair Play Regulations," said the statement from CAS.
"An arbitration procedure will now be initiated and will involve an exchange of written submissions between the parties while a panel of CAS arbitrators is convened to hear the appeal.
"Once the panel has been formally constituted, it will issue a procedural calendar. It is not possible to say at this time when the arbitral award for this matter will be issued.
"CAS will not provide any further information in relation to this procedure, except to issue a media release announcing the panel's decision."