Zia-ul-Haq Amarkhail, head of the secretariat of the Independent Election Commission (IEC), denied all charges against him but said he was stepping down to save the election process.
Presidential candidate Abdullah Abdullah has boycotted the counting of votes from the run-off election a week ago, accusing the IEC of being biased against him in the contest against his rival Ashraf Ghani.
"Now the door is open for us to talk to the (election) commission and talk about the conditions and circumstances that will help the process," Abdullah told reporters after Amarkhail resigned.
Abdullah had called for Amarkhail's removal since the June 14 vote, which was at first hailed by the US and other international allies as a major step forward in the country's first democratic transfer of power.
Abdullah's campaign team yesterday released telephone recordings that it said were conversations of Amarkhail arranging ballot-box stuffing using the code words "sheep stuffing".
"I have resigned only to protect the election process, and so that Dr Abdullah Abdullah can put an end to his boycott and resume his relationship with the IEC," Amarkhail said at a press conference.
A smooth election is seen as a benchmark of success for the US-led coalition that has fought against the Taliban and donated billions of dollars in aid to Afghanistan since 2001.
International diplomats expressed alarm over the prospect of a disputed poll result and the risk of unrest as military assistance and civilian aid declines.
Pro-Abdullah demonstrators took to the streets of Kabul on Saturday, and the UN mission warned that any civil unrest "could lead to a spiral of instability".
It has also tried to reduce tension by asking Afghans not to incite violence with comments on Twitter or Facebook.
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