Turkish poll body Erdogan's party challenge on sacked voters
However the electoral council, known by its Turkish initials YSK, did accept an "extraordinary" appeal by the ruling Justice and Development Party (AKP) for over 41,000 voters and election officials in Istanbul to be investigated, state news agency Anadolu reported.
Erdogan loyalist and former prime minister Binali Yildirim failed to clinch the Istanbul mayor's post at the 31 March local elections, as voters punished the AKP following last year's currency crisis and double-digit inflation.
The opposition was more unified than in previous elections, with analysts saying the support of Kurdish voters helped the main opposition candidate Ekrem Imamoglu win Istanbul.
The AKP also lost to the opposition in Ankara but remained the most popular political party nationwide in the polls.
The defeat in Istanbul is especially sensitive for Erdogan who made his political career as a successful and popular mayor of the city.
Because of this, the AKP party filed two appeals, to cancel and re-run the Istanbul mayoral elections.
The ruling party's first request to cancel and re-run the mayoral election was still pending when AKP deputy chairman Ali Ihsan Yavuz told state news agency Anadolu the party had submitted a second petition.
This petition was based on more than 14,000 people who had previously been dismissed from public sector posts under an emergency decree having voted in the election.
The second appeal was made on Saturday.
"The AKP is making a mockery of what remains of Turkey's democratic electoral system by attempting to use a system designed for legitimate suspicions of electoral fraud or irregularities to delegitimase the results of Istanbul's local elections, or worse, have them cancelled. It is clear at this point that the legitimate winner of these elections was Ekrem Imamoglu", an anonymous analytical source told The New Arab.
"With today's decision, the YSK has again proven that it still operates as an - at least partially - independent body, despite the immense pressure put on it and the fact that its members are essentially hand-picked by the AKP and its ally the MHP. Any streaks of independence in such crucial institutions is a sign of hope for a Turkey marred by democratic backsliding over the past few years", they added.
Turkey's electoral authority has already banned members of the pro-Kurdish People's Democratic Party (HDP) from assuming positions won in the local elections due to their having been fired under the emergency decree.
More than 140,000 people were dismissed from public sector jobs following a coup attempt in 2016, which Ankara blames on US-based Muslim cleric Fethullah Gulen.
The AKP or its predecessors had held Ankara and Istanbul since 1994.
After a failed 2016 coup against Erdogan, more than 140,000 individuals were sacked or suspended from the public sector, including teachers, over alleged links to coup-plotters.
But the challenge to the validity of sacked public workers' votes was rejected, Anadolu reported.
The AKP's wider appeal, for a repeat of the entire Istanbul vote, still awaits a ruling by the YSK.
Imamoglu was given his election mandate last week after defeating Yildirim by around 14,000 votes in Istanbul following days of recounting because of AKP appeals.