The statement did not say what offensive remarks had been made in the programme, which was moderated by Al Jazeera's Faisal al-Qassem.
Sultan has drawn strong criticism for her controversial views on how Islam needs to be reinterpreted to suit the modern world.
Protests have raged across the Muslim world since several Danish newspapers recently reprinted a drawing featuring the prophet.
The cartoon, first published in early 2006, caused days of protests worldwide, including in Afghanistan, where 11 people were killed.
Al Jazeera is based in the Gulf state of Qatar.