Invalid counting sheets, not deploying civil servants at polling centres are the main reasons cited for a revote of March polls.
Turkey's top election body on Wednesday justified the Istanbul revote to be held on June 23.
Some 30,281 voters in 108 ballot boxes were declared invalid due to a lack of or unsigned counting sheets, the Supreme Election Council (YSK) said in a statement.
"The lack of counting sheets in 108 ballot boxes, which is one of the most important factors in determining the election results, seriously damages the reliability of the election results in these boxes," it added.
Also polling clerks who were not civil servants served in 754 polling centres in the March 31 mayoral elections in Istanbul.
The council said this unprecedented practice would affect the vote difference of 13,729 between the ruling and opposition alliances.
The results of the March Istanbul vote were cancelled after the governing Justice and Development (AK) Party and its coalition partner Nationalist Movement Party (MHP) appealed, citing irregularities and contradictions with the country's election law.
The mayoral certificate of Ekrem Imamoglu, the opposition Republican People's Party's (CHP) candidate, was annulled by the YSK on May 6.
The election body also announced the overall official results of the March 31 local polls.
According to the official results, AK Party won 15, CHP 10, HDP three and MHP one of the metropolitan municipalities, discluding Istanbul in which the polls were to be redone on June 23.
In other cities, the AK Party won 742, CHP 240, MHP 233, HDP 57, IYI (Good) Party 24, Felicity Party 21, the Great Unity (BBP) Party 10, Democrat Party (DP) eight, the Democratic Left Party six, the Communist Party of Turkey one and independent candidates 13.