Supreme Electoral Council head Sadi Guven said the recount will mostly focus on invalid votes.
CHP officials halted the recount process in Istanbul earlier this week but the Supreme Electoral Council ruled that the recount should resume.
One of the disputed races is for mayor of Istanbul, where CHP candidate Ekrem Imamoglu has a 22,000-vote lead over AK candidate Binali Yildirim. Imamoglu received 48.79 percent of the vote while Yildirim has 48.51 percent.
Imamoglu called on the Supreme Electoral Council to carry out its recount but also give him the mandate as elected mayor. He said he believes the recount will affect both candidates but the results won't change.