The Ivory Coast international is set to leave for the tournament which starts on January 19, while the Italian isn't sure whether his captain will be fit for the weekend.
The Italian had hoped that his destructive midfielder would miss the tournament held in South Africa or that he would be available for their Premier League clash against Arsenal on January 13.
However, it seems that Toure will stay in Manchester up until City's FA Cup third round match against Watford on January 5, then he will join up with his Ivory Coast team-mates.
Mancini told reporters: “It is difficult. I think he will go to the African Nations Cup after that game.”
That defeat meant City is now six points behind their rivals in the Premier League, but Mancini insists he has full belief in his players to turn their fortunes around.
"We showed that we were better than Manchester United," he said. “But they have more experience than us and it is not a problem to them when they fall behind.
He added, “We need to work hard but we can recover this position. By February everything could have changed.”