The Italian forward is reported to be deeply unhappy at the cartoon and the Gazzetta dello Sport has apologised.
A spokesman for anti-discrimination group Kick It Out said: "Mario's very presence in the Italian team is symbolic on so many levels. The Italian media ought to champion this individual rather than singling him out as a scapegoat and somehow inferior to his international team-mates."
The drawing - published on the day of Italy's Euro 2012 meeting with England - showed Balotelli on top of Big Ben in a reference to King Kong on New York's Empire State Building. It has led to a number of complaints from readers prompting the newspaper to apologise.
A statement from Gazzetta read: "Some of our readers have protested regarding (Valerio) Marini's cartoon.
"Balotelli was depicted as King Kong. We can honestly say it was not among the best products of our talented cartoonist.
"At this time, a measure of prudence and good taste are necessary because everything, absolutely everything, can be misinterpreted.
"The newspaper is for those who read it and hence, if certain readers found the cartoon offensive, we apologise.
"But those that accuse Gazzetta (and poor Marini) of racism are going overboard. This newspaper has fought any form of racism in every stadium and has condemned the boos directed at Balotelli as an unacceptable form of incivility."
Balotelli, who has been a reported target of racist chants at Euro 2012, said at the start of the tournament in Poland and Ukraine that if he heard himself being racially abused he would consider walking off the pitch.