Pastor Brian Houston said he had taken the decision to remove Mr Driscoll's invitation after "personal interaction".
It comes after a petition to ban him from the event gathered almost 3,000 signatures.
Media reports in recent days accused Mark Driscoll of likening women to "penis homes".
Mark Driscoll quit American mega church Mars Hill church last year after it found him "guilty of arrogance, responding to conflict with a quick temper and harsh speech, and leading the staff and elders in a domineering manner".
In a statement the head of Hillsong, Pastor Houston said: "Clearly Mark has held some views and made some statements that cannot be defended.
"One or two of the more outrageous things he is purported to have said, I have heard for the first time through the media exposure over the past week."
The statement said: "The teachings of Christ are based on love and forgiveness, and I will not write off Mark as a person simply because of the things that people have said about him, a small minority of people signing a petition or statements he has made many years ago for which he has since repeatedly apologised.
"However, I do not want unnecessary distractions during our conference, particularly as this 30 minute interview was only a small part of this five day event.
"It was clear to me that Mark's attendance had the potential to divert attention from the real purpose of Hillsong Conference, which is to see people leave encouraged in their own spiritual journey."