A preliminary enquiry has been opened by a court in the southern city of Marseille, with police fraud officers working in conjunction with the Central Office for Fighting Serious Financial Crime (OCRGDF).
"Like hundreds of other French companies, Olympique Marseille were the victims of a scam," the club said in a statement, adding they had "immediately filed a complaint" and "taken all the necessary steps".
"Part of the money has been recovered," the statement added.
It is estimated that 360 French businesses have been hit by fake transfer orders, representing €300 million ($340m), in the past two years.
A delegation from the French Justice Ministry visiting Beijing last November estimated that there was "an acceleration of such cases in late 2013, early 2014".
Other recent high-profile victims of the scam were French international tyre-maker Michelin, to the tune of €1.6m ($1.8m), and global audit firm KPMG, who lost €7.6 ($8.6m).
The scam is the latest misfortune to hit Marseille who were in the headlines recently as part of a probe into suspect player transfers.
Jose Anigo, the club's former sporting director, was released without charge last week after he was among 12 people arrested as part of an enquiry involving players agents as well as suspected crime figures.
The suspect transfers being investigated date back to 2010 and include that of French international striker Andre-Pierre Gignac.
The club management has since changed. But president Vincent Labrune as well as several former leaders were among people held for questioning in November.