Law 10.4 (b) - Stamping or trampling: A player must not stamp or trample on an opponent.
Flannery, who has been named in the extended Ireland Six Nations squad, said that he did not intentionally stamp on any player during Munster's 26-19 defeat to their French pool rivals.
One of the Clermont Auvergne players, flanker Alexandre Audebert, has also been cited for his part in two incidents during Sunday's game.
The first alleges that he stamped/trampled on Ronan O'Gara, leaving the Munster out-half with a severed ear that required 20 stitches, and the second citing is for an alleged punch on Munster replacement flanker Alan Quinlan.
The ERC have yet to confirm when Flannery's hearing will take place but, in a statement, the tournament organisers said that "the independent Disciplinary Committee will be appointed as soon as practicable."