Uefa said the investigation “will focus on several alleged violations of FFP that were recently made public in various media outlets”.
German news magazine Der Spiegel has published a series of claims, based on leaked documents, that Premier League champions City have violated FFP rules.
“The accusation of financial irregularities is entirely false.”
The club added:
“Manchester City welcomes the opening of a formal Uefa investigation as an opportunity to bring to an end the speculation resulting from the illegal hacking and out of context publication of City emails.
“The club’s published accounts are full and complete and a matter of legal and regulatory record.”
Uefa previously found City had breached FFP rules in 2014.