Flannery, who was an original selection for the 2009 Lions before an elbow injury forced his withdrawal prior to departure for South Africa, will face a disciplinary hearing later this week after being cited for an alleged kick on French wing Alexis Palisson during the 33-10 reverse in Paris.
Referee Wayne Barnes awarded France a 23rd-minute penalty as a result of the incident but Flannery did not receive either a yellow or red card.
No exact date has yet been set for the 31-year-old's hearing but, if found guilty, he would likely miss at least two Magners League fixtures and two Six Nations ties.
The minimum suspension for the offence is four weeks, which would prevent Flannery from appearing in Munster's domestic ties with Edinburgh and the Dragons, as well as Ireland's trip to face England at Twickenham and their Round 4 encounter with Wales at Croke Park.
The mid-range sanction for the offence is an eight to 12-week ban, which could stop Flannery from featuring in Munster's attempts to retain their Magners League crown, while the maximum length of suspension for the offence is a full calendar year.