The AKP demanded a recount in Ankara and Istanbul citing irregularities after tallies showed the party was defeated in both cities in what would be a major setback in a decade and a half in power.
Erdogan's remarks appeared to signal more AKP challenges over Istanbul, the country's economic hub and largest city, echoing commentary in pro-government media last week denouncing a "ballot box putsch" during the March 31 election.
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"We are seeing that some organised crimes have been carried out," Erdogan said at a press conference before a trip to Russia, without giving details. "There is an element of robbery in all of this. There was some theft at the ballot box."
In the capital Ankara, the Supreme Electoral Council on Monday officially handed opposition CHP party candidate Mansur Yavas his mandate, an AFP reporter said.
Erdogan's AKP won most votes nationwide in the election, but voters appeared to punish the party in the two big cities with Turkey's economy in recession and inflation in double digits after a currency crisis last year.
Defeat in Istanbul would be especially sensitive for Erdogan who grew up in one of its working-class districts and began his political career as mayor of the city.
AKP's candidate for Istanbul former premier Binali Yildirim and opposition CHP's Ekrem Imamoglu both declared victory soon after the Istanbul race when initial results showed a dead heat.
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Electoral authorities later said Imamoglu was winning by around 20,000 ballots, but that gap has narrowed during a week of recounting. Both parties say the difference is now less than 17,000 ballots. The two candidates each received more than 4 million votes.
Imamoglu has declared himself Istanbul mayor and called on the AKP to accept the result.
Erdogan said when there was a problem with a percentage of votes in other countries, appeals and even new elections were not unusual.
"No one has the right to declare themselves victorious with a difference of around 13,000-14,000 votes," Erdogan said of the Istanbul results. "As for the irregularities, it was not just in some places, almost all of it is irregular."
After 16 years in power, Erdogan is praised by supporters, especially among his base with more religiously conservative Turks who say he oversaw a period of economic growth and prosperity.
But his critics at home and among Western allies say the Turkish leader has undermined democracy by purging dissent especially in the wake of a 2016 failed coup Ankara blames on a US-based Muslim cleric.
Erdogan campaigned hard portraying the local vote for mayors and district councils as a fight for the nation's survival, but the election became a test of AKP's support after an economic slowdown hit Turkey.
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