The Italy international is understood to have angered Mancini with a late challenge on team-mate Scott Sinclair at the club's Carrington base.
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The 48-year-old confronted the centre-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 rumoured 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.
"I think Mario will stay but the future depends mostly on him," Mancini told La Gazzetta dello Sport last week. "Sheikh Mansour likes Balotelli because he recognises the talent and he exports the name of the City over the world.
"We need to consider that Mario was made as a major investment, and this is not a club that throws its capital through the window.
"The relationship between me and him is always good, even if one day he does something," he continued.
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"I love him because for many years we live together. I've seen him grow. But the professional relationship is another thing and I've told Mario what I need from him.
"The time of cheap talk is over. Balotelli is 22 years old and now it's time to be professional. I ask from him seriousness and commitment in training, a more stable private life and correct behaviour on the pitch."
Balotelli has been out of the first-team picture due to an illness recently, and was set for a return to the side when City face Watford in the FA Cup on Saturday, before Thursday's incident.