England won Sunday's last 16 tie 3-0 but the game at Valenciennes was marked by Cameroon players' furious response to several refereeing decisions,.
At one stage they apparently threatened to walk off the pitch.
A spokesperson for football's ruling body confirmed "proceedings have now been opened by the FIFA Disciplinary Committee against the Cameroonian Football Association."
He added the investigation focused on "alleged breaches related to article 52 (team misconduct) and article 57 (offensive behaviour and fair play) of the FIFA Disciplinary Code".
England coach Phil Neville said after the encounter he was left "utterly ashamed" by the behaviour of the Cameroon players.
Cameroon coach Alain Djeumfa said his team had been the victims of an "injustice".
Their anger reached boiling point when Ellen White's goal to make it 2-0 in first-half stoppage time was initially disallowed for offside before being awarded after Chinese referee Qin Liang consulted with the Video Assistant Referee.
Their players surrounded the referee, pointing to the big screen replays of Read More
