The affair relates to Chelsea's decision to leave Ballack out of their Champions League squad, meaning he can not play for them in the competition until February.
Reports have since emerged that the German midfielder is much closer to recovering from injury, but Mourinho has revealed this is not the case, but stressed that he would want to play Ballack if he was available.
In typical Mourinho fashion the Portuguese said: "I was at home taping games and trying to watch my players' matches and I was also reading a little about general football issues.
"One of them caught my eye, it was obviously the Michael Ballack story, where at one point I thought 'He is ready to play. If anyone can be critical of Chelsea for leaving him out of the Champions League list it is because a miracle happens and he is ready to train and play!'
"So on Tuesday, the first thing I did was to go and see him but I was surprised he was not ready to train, he was like he has been for the last four months, in the medical room."
He added: "Do I want him to play? Of course yes. Last season, against a sea of critics, I was the only one behind him, so this season where I am playing with wingers and where he could make a top contribution to our game I don't want him?
"If he is fit or if the medical department thinks he is ready to play football in the next couple of months, do we leave him out of the Champions League list?
"Of course not. I miss him on the pitch. Since April I only see him in the medical room and sometimes at lunch in the canteen.
"Because I am not a doctor, the Chelsea doctor reports that the player will not be ready to play in most games in the Champions League group, what do I do? Believe in the Chelsea doctor or believe in others? The answer is simple.
"Let's wait and see when Michael is ready to play football again for Chelsea."