The Italy international is understood to have angered Mancini with a late challenge on teammate Scott Sinclair at the club's Carrington base. The 48-year-old confronted the center forward and the pair had to be separated by staff before Balotelli left Carrington shortly after.
Balotelli has been involved in altercations at the club's training ground before, having previously been photographed clashing with Micah Richards.
The striker has been linked with a potential January exit from Manchester City, with AC Milan rumored to be interested in making a bid.
Until now, Mancini - one of the controversial star's staunchest defenders - has insisted the 22-year-old would not be sold, but recently indicated Balotelli had to work harder in training.