The organisation, which attempts to combat discriminatory behaviour, including racism, in English football, released a statement on Tuesday (AEDT) following Nice's 3-2 defeat to Dijon over the weekend.
Balotelli was cautioned in the 74th minute of that Ligue 1 encounter, with Nice claiming his punishment came after informing referee Nicolas Rainville of racist chants from Dijon fans.
"Mario Balotelli has inherited a yellow card, after... getting annoyed with racist insults from the public," read a tweet from Nice at the time, and Kick It Out called for action to be taken against the officials in question.
"Kick It Out was shocked to see Mario Balotelli booked for bringing to the attention of the referee alleged racist chanting directed towards him by Dijon supporters," a statement read.
"It is unacceptable and wrong to see that once again, a match official has failed to apply the UEFA protocol – in place for a number of years – which requires action to be taken to stop the game to deal with the offending abuse.
"Although Kick It Out's remit is within English football, the organisation has contacted anti-discrimination network Football Against Racism in Europe (FARE) to see what actions they will be taking in raising this with Ligue 1 officials.
"The organisation expects a strong response from the French football authorities in condemning both the alleged racist chanting from Dijon supporters and the failure of the referee to follow protocol to halt the behaviour, as well as the decision to compound Balotelli's experience as a victim by booking him for merely asking the match official to do his job."