Milan, who sit in 12th position and are already 13 points behind league leaders Roma, had been set to welcome Balotelli back from a three-game ban.
However a thigh problem suffered in training means the Italy international is expected to sit out Saturday's league fixture at home to Udinese and could be doubtful for Tuesday's visit of Barcelona to the San Siro.
A brief statement by Milan said: "Mario Balotelli has reported a muscular pain in his right thigh. The player will be monitored in the following days to ascertain the extent of the problem and the appropriate treatment."
After two games in Group H, Milan, on four points, sit second behind the Spanish giants after a win against Celtic and a draw away to Ajax.