The police used tear gas as the fans let off flares and threw bottles outside a restaurant in Milan where the Italy striker was having a dinner.
One policeman was taken to hospital with head injuries, reports say.
Balotelli is in Milan for a medical before a proposed transfer for an initial fee of 22m euros (£19m).
Balotelli said earlier he had no hesitation about deciding to move from England to the seven-time European champions.
“I’d wanted to play for Milan for such a long time,” said the 22-year-old.
“Obviously I played for other teams and couldn’t come. But when there was the chance, I ran.”
City signed Balotelli from Inter Milan – AC Milan’s arch-rivals – for £24m in 2010 and he scored 30 goals in 80 appearances for the club.
He helped City to the Premier League title last season, but has managed only three strikes in 20 matches this time round.
Milan reached an agreement with City on Tuesday, and Balotelli is expected to sign a four-and-a-half-year contract, subject to passing his medical.
Balotelli’s departure follows a training ground altercation with City manager Roberto Mancini on 3 January – the latest in a series of controversies during his time at the club.