The alleged clash, which was caught on camera by photographers, again casts doubt over the striker's future at the Premier League-winning club.
Mancini apparently lost his temper with his Italian compatriot after Balotelli made a reckless challenge on team-mate Scott Sinclair at the club's Carrington training base on the outskirts of Manchester.
Pictures show Mancini gripping Balotelli's orange bib in an apparent rage, before the two men are separated by members of the coaching staff.
An eyewitness, quoted in the Manchester Evening News, said: "Mancini ran at him – he was furious. He grabbed hold of him and appeared to try and throw him on the floor.
The pair were separated by coaching staff (Pic: Eamonn and James Clarke)
"It looked like Mario was too strong and he couldn't get him down. Then all the coaches ran in to separate them but Mancini was having none of it. He kept trying to break free and have a go at him again."
Balotelli was also pictured walking to his car in the car park after the end of the session.
The 22-year-old has been no stranger to controversy since he arrived in Manchester from Inter Milan in 2010.
Just days after signing for City, he hit the headlines after crashing his Audi R8 en route to the club's training ground.
He was found to be carrying £5,000 in cash at the time of the accident and when police asked why, he reportedly replied: "Because I am rich."
In October 2001, the Italian had another run-in with the emergency services after a firework was set off in the bathroom of his home, triggering a fire.
The next day, he scored in the Manchester derby and celebrated by revealing a T-shirt with the words: "Why always me?"
The player celebrated a goal by showing his T-shirt
In December 2011, Balotelli broke a club 48-hour curfew by visiting a curry house ahead of a match against Chelsea. Just days later he attracted more negative headlines after pictures emerged of a training-ground bust-up with team-mate Micah Richards.
Balotelli has twice been dropped from City's match-day squad this season and Mancini has repeatedly warned him he is in danger of wasting his talent.
In December, Balotelli dropped a legal action against City after taking them to a Premier League tribunal in an attempt to overturn a fine of two weeks' wages over his poor disciplinary record last season.
Mancini also chastised him after a sloppy performance in City's 3-2 loss to Manchester United in last month's Manchester derby, in which he was substituted in the 52nd minute.
"I love Mario like a guy, and as a player, but I think it's important for him to start to think about his job if he wants to play well," said Mancini.
"When you have a player with Mario's quality, you can't believe that he throws his quality out of the window.
"I've seen players in my life with fantastic quality who ended up with nothing and I don't want Mario to finish like these players, because it will be bad for him."
Balotelli is yet to play since that game, with a virus having ruled him out of City's festive fixtures, but he could feature in Saturday's FA Cup third-round tie against Championship side Watford.