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 the trip to Newcastle.
Kompany picked up a groin injury against Manchester United last Sunday.
And while City will give the Belgian every chance of making the trip to St James' Park, Mancini does not expect him to make it.
"We will try but it is difficult," said Mancini. "Probably two percent chance."