According to preliminary results, opposition parties had won or were ahead in nine races, many of them in small communities, and Prime Minister Tayyip Erdogan's AK Party appeared to have won four of the races that the High Election Board (YSK) ordered be held again.
The AK Party dominates the Turkish political landscape, controlling most municipalities and a large majority of the seats in parliament.
Erdogan has said his party's success in the March poll had renewed his mandate after 11 years in power when AK Party candidates netted 45 percent of the overall vote, despite a year of anti-government protests and a corruption scandal that implicated the three-time premier's inner circle.
In a closely watched raced, Sirri Sakik, a lawmaker from the pro-Kurdish Peace and Democracy Party (BDP), won 51 percent of the vote in the race for mayor in the remote city of Agri near the Iranian border besting the ruling AK Party's Hasan Arslan, with 99 percent of ballots counted, NTV news channel reported.
The YSK did not cancel every disputed race, including a close one in the capital Ankara that was marred by allegations of voter fraud, declaring the AK Party incumbent the victor.