The midfielder has made 12 Ligue 1 appearances so far this season - nine of which have come from the start - but earlier in December made public his desire to secure a loan move away in the upcoming transfer window.
His comments angered the official, who wants him to remain at the club and go on to take the armband in the future.
"I was very disappointed, I told him to his face. His statements were unacceptable," Al-Khelaifi told Le Figaro.
"It's a total lack of respect towards the club that has done so much for him. I will never accept that he considers himself more important the club.
"He is a great talent. My dream is that he will become PSG captain one day, but he needs to respect the club, the coach and his team-mates.
"He's got the message and will certainly stay in January."