The 22-year-old striker has run into trouble with boss Roberto Mancini at Manchester City after several high-profile incidents, and looks increasingly likely to be surplus to requirements at the Etihad.
But Mourinho has stood up for the controversial forward, claiming that his behavior was wrongly interpreted by all quarters.
"Balotelli, [Zlatan] Ibrahimovic, [Marco] Materazzi. They are not the most difficult of players to manage," the newly-turned 50-year-old commented to Rai Sport. "With Balotelli, it was even fun.
"Those not seen or felt outside are in fact the difficult [people], rather."
Mourinho's position in Madrid has come under scrutiny of late, as reports of a player mutiny against the embattled trainer surfaces.
But he refused to be daunted by the challenges at hand, and instead spoke of his desire for fresh success in European competition, even beyond his time with the Spanish champions.
"I cannot say what I want to conquer this season, but I hope to win my third Champions League [following success with Porto and Inter]," the Portuguese concluded.
"I do not know if it will be with Madrid this year, because it is all very balanced. Still, I have another 20 years of football to achieve my target."