The Supreme Electoral Council (YSK) "rejected our call for all votes to be recounted in Istanbul," the AKP's Ali Ihsan Yavuz said on Twitter. "It is incomprehensible for a decision like this to be made when the irregularities are clear to see."
Erdoğan on Monday questioned the results – 48.8% for the CHP and 48.55% for the AKP - , claiming that the result was incorrect as a result of "theft" at the ballot box and "organised crimes" that were carried out in Istanbul.
The AKP already lost the capital Ankara. Defeat in Istanbul, the country's largest city, would be another blow to Erdogan's party after a decade and a half in power.
Both Istanbul candidates claimed victory after preliminary tallies were neck and neck.
Electoral officials later said Imamoglu was ahead but the gap has narrowed to around 15,000 votes.
“Erdogan’s frequent motto ‘whoever wins Istanbul, wins Turkey’ can easily be turned into ‘whoever loses the cities, loses Turkey'," political commentator Serkan Dermitas wrote in the daily newspaper Hurriyet, saying that it is the first time that Turkey’s political parties fought each other in two alliances: the AKP together with the nationalist MHP in the People's Alliance, and the main opposition Republican People’s Party CHP with the IYI (“Good”) Party and the pro-Kurdish People’s Democratic Party (HDP) in the Nation Alliance.
Nationwide, the People’s Alliance had 51,64 percent of the vote against the Nation Alliance with 37.57 percent.
Recep Ozel, the AKP's representative on the Supreme Electoral Council board, told reporters in Ankara early Tuesday that the council accepted the party's claim of "irregularities" in ballot boxes.
But there would be only a partial recount of 51 ballot boxes in 21 Istanbul districts.
The AKP had called for a full recount in most of the 39 districts of Istanbul, but the council rejected that.
A decision for one Istanbul district, Buyukcekmece, had been delayed because of an investigation into fraud claims.
Istanbul police were investigating claims that 11,186 people changed their addresses to Buyukcekmece before the local elections, DHA news agency reported.
Ozel also said the difference between Imamoglu and Yildirim was now just 14,604 ballots, while the latest figures from the CHP suggested the difference was around 15,000.
Electoral authorities last week said Imamoglu was ahead by 28,000 votes before the recount of void ballots begun.
A CHP official said the electoral council's decision would "not affect" the result for Imamoglu.