OC Home Front Command Maj.-Gen. Yair Golan issued an order on Monday banning Sheikh Raed Salah, head of the Islamic Movement's northern branch, from entering Jerusalem over the next three weeks.
Salah will have the opportunity to appeal to the decision.
If the ruling remains in place, the IDF said that Golan planned to extend it by an additional six months.
Golan issued the order after reviewing intelligence information that Salah was a threat to public safety and in accordance with the recommendations of relevant security agencies.
In just a few days, Salah is due to be sentenced for assaulting a policeman during a riot in the capital's Old City nearly two years ago.
The incident took place in February 2007, near the Dung Gate, when Salah and four other Israeli Arabs allegedly took part in riots in protest of Israeli archaeological excavations that were being conducted next to the Mugrabi Gate.
Salah found himself in legal trouble recently as well, when police accused him of fomenting unrest in the Old City during Succot.
Scores of rioters were arrested and a number of police officers were injured in disturbances that sprang up throughout east Jerusalem, including in the Muslim Quarter of the Old City. Salah, who was arrested at the time, was found guilty of incitement and barred from the Old City for a limited period.
Abe Selig contributed to this report