Zia ul-Haq Amarkhail said he was stepping down “for the sake of national unity”, denying allegations of ballot box-stuffing earlier this month.
His resignation comes after audio tapes were released allegedly revealing that Zia ul-Haq Amarkhail was trying to influence the outcome of the vote.
They were published by the camp of one of the candidates – Abdullah Abdullah.
However, Abdullah Abdullah’s rival Ashraf Ghani has also made allegations of fraud.
The official results of the June 14 run-off are yet to be published.
In a dramatic turn of events on Monday, Zia ul-Haq Amarkhail tendered his resignation on national television.
He vehemently denied any wrongdoing, saying he had been the victim of a plot.
Zia ul-Haq Amarkhail also described the tapes as “fake” and blamed the country’s security services for interfering in the election.
In an apparent reference to ballot box-stuffing, the tapes appear to show Zia ul-Haq Amarkhail urging a colleague to “bring the sheep stuffed and not empty”.
The reference to sheep and goats – ballot boxes and people or votes – is made several times during the recorded exchanges.
Reacting to the latest developments, Abdullah Abdullah said the resignation of Zia ul-Haq Amarkhail had opened the door for discussions with Afghanistan’s Independent Election Commission.
Abdullah Abdullah also said his recent decision to stop co-operating with the election authorities had not been intended to disrupt the process, but to prevent a fraudulent election result and to protect people’s votes.
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