The ruckus follows similar disputes between different ultra-Orthodox groups, YnetNews.com reported Tuesday.
The news site reported police were sent to the scene when clashes broke out and the ultra-Orthodox protesters threw stones.
Later in the day, a group of ultra-Orthodox residents, who object to Haredi voters, clashed.
Most of the ballots in Jerusalem's ultra-Orthodox neighborhoods were labeled "sensitive." Authorities were dispatched to prevent voter fraud.
Ultra-Orthodox candidate Knesset Member Meir Porush was projected to be losing to businessman Nir Barkat. Meanwhile, in Tel Aviv, Mayor Ron Huldai was being challenged by Knesset Member Dov Khenin.