The Inter president questioned the quality of refereeing in Serie A on the back of a recent defeat to Atalanta in which the away side were given a dubious penalty
Inter were beaten 4-3 by Atalanta at San Siro last Sunday, despite leading 3-1 at one stage, with the visitors awarded a penalty on their way back into the game.
That prompted Moratti to rage about the performance of officials after the game, claiming "when they want to hit you, you get hit" and suggesting his side were being targeted by referees.
The FIGC have now decided to delve further into his comments and released a statement on Friday confirming the beginning of disciplinary proceedings.
"Moratti has been referred [to the disciplinary authorities], for having expressed judgements that harm the reputation of and in particular the good faith and impartiality of match officials and consequently , the credibility of the championship due to the work of the referees.
"The comments harm the reputation of organisations operating within the FIGC and the prestige and credibility of the federation itself."
Last weekend's result leaves Inter in sixth place in Serie A with 50 points from 31 games.