Yavuz underlined that a greater number of votes had been disqualified in districts where AK Party had won, including Istanbul.
The opposition candidate for Istanbul mayor, Ekrem Imamoglu was leading by almost 28,000 votes with most ballot boxes counted, Supreme Election Board (YSK) chairman Sadi Guven said though final results would confirm the victor.
Other early results appeared to show losses for the pro-Kurdish People's Democracy Party (HDP), which lost at least three cities, Sırnak, Agri and Bitlis, in its southeastern heartland to the AKP.
He has been the country's most popular - although divisive - modern politician, tightening his grip in elections previous year that ushered in a powerful executive presidency that alarmed Western allies who fear growing authoritarianism in Turkey.
The CHP took over the capital after 25 years, which was governed by the ruling party AKP since it came to the rule.
AK Party's Istanbul candidate Binali Yildirim told reporters on Monday that invalid votes cast on Sunday outnumber the vote difference tenfold, adding that his rival Ekrem Imamoglu - the candidate of the main opposition Republican People's Party (CHP) - now had 25,000 more votes.
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Sezgin Tanrikulu, a CHP MP from Istanbul, said that although Imamoglu won the race in Istanbul, the election board was waiting for the objection period to end for legal reasons to declare the official victor. The AKP has said there were problems with many votes in both cities, and it would appeal results in every Ankara district.
Following the last week's prediction of JPMorgan, there had been intense volatility on the USD/Turkish Lira pair throughout last week and the Turkish currency had weakened as far as 5.6750 against the American dollar, which eventually had brought back memories of last year's currency crisis.
Defeat for Erdogan's Islamist-rooted party in Ankara was a significant blow for the president.
After 99% of the votes were counted in Ankara, Mansur Yavash, representing the opposition Republican People's Party (NPP), won 50.89%, while AKP member and incumbent Mayor Mehmet Ozhaseki made 47.06%, Turkish state news agency Anadolu reported on Monday, April 1. The AK Party said former Prime Minister Binali Yildirim defeated his CHP rival Ekrem Imamoglu by a mere 4,000 votes - with both candidates polling more than 4 million votes.
But the recent economic troubles took a toll on party support, two AK Party sources said, after the lira slumped against the dollar past year, inflation jumped to 20 percent, unemployment climbed and the economy tipped into recession.
"Political Islam's quarter-century old hegemony in Turkey's two largest cities is over", he said.
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"If (Erdogan) can not create a solution, it's inevitable that there will be greater losses in the period ahead", another party source said.
The main opposition party winning the race for metropolitan mayor in Ankara marks a symbolic shift.
He commended the Turkish public for the high turnout rate of 84% and called it a "sign of healthy democratic interest and awareness".
He said the party would work to understand and fix where they failed.
"If we have objections [with the electoral commission], we will raise them".
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