Recep Tayyip Erdogan’s government has been accused of authoritarianism and corruption after a string of scandals.
The local elections, the first vote since mass protests last June, were seen as a barometer of his popularity.
Recep Tayyip Erdogan was not standing for election but campaigned hard for his Justice and Development Party (AKP).
With over 60% of the votes counted, it was leading the main opposition party 47% to 27%.
The AKP had been aiming to equal or better its 38.8% share of the vote in the last local elections in 2009.
Speaking from a balcony at his party’s headquarters in Ankara, Recep Tayyip Erdogan thanked his supporters.
“You stood up for Turkey’s ideals… for politics, for your party and your prime minister,” he said.
But he warned he would “enter the lair” of enemies who had accused him of corruption and leaked state secrets.
“They will pay for this,” he said.
Voting in the local assembly and mayoral elections passed off peacefully in most areas, but eight people were reportedly killed in two separate incidents involving supporters of rival candidates.
Feuding families were said to have clashed in the southern city of Hatay and the eastern province of Sanliurfa.
PM Recep Tayyip Erdogan has been eyeing a run for the presidency in August – the first time voters will directly elect the head of state – or may seek to change the rules to allow him to seek a fourth term in office.
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