Mancini had been hoping the midfielder would opt against going to the tournament in South Africa. However, the City boss now concedes Toure will leave after the FA Cup tie with Watford on January 5.
"It is difficult," said Mancini. "I think he will go to the African Nations Cup after the Watford game."
Meanwhile, Mancini believes skipper Vincent Kompany has only a 'two percent' chance of being fit for Saturday's trip to Newcastle.
And whilst City will give the Belgian every chance of making the trip to St James' Park, Mancini doesn't expect him to make it.
"We will try but it is difficult," said Mancini. "Probably two percent chance."
City head to the north-east six points adrift of United following last weekend's game at the Etihad Stadium.
Yet despite that 3-2 defeat, Mancini insists he has total belief in his squad, and that City actually proved themselves to be the superior side no matter what the result.
"We showed that we were better than Manchester United," said Mancini. "But they have more experience than us and it is not a problem to them when they fall behind. We need to work hard but we can recover this position. By February everything could have changed."