The England international has been on the fringes of things for City this season, making only one Premier League start and another late appearance as a substitute but he remains a valuable member of boss Roberto Mancini's squad.
The Italian admits he does not know how long Milner might be out for, saying: "Milner has a problem in his toe. He has pain. He will see a specialist on Monday and after that we'll decide what to do."
Defender Maicon also missed Sunday's clash after receiving a kick in Tuesday's defeat by Real Madrid and will miss Tuesday's League Cup tie against Aston Villa.