Zia ul-Haq Amarkhail told reporters today that he denies any involvement in fraud but he is stepping down "for the national interest."
One of the two candidates, Abdullah Abdullah has said his campaign monitors had recorded ballot box stuffing and other irregularities. He suspended cooperation with the vote counting process and demanded Amarkhail be suspended.
The crisis has threatened what Western officials had hoped would be a peaceful transfer of authority.
Amarkhail defended the conduct of the June 14 balloting and called on Abdullah to resume relations with the Independent Election Commission and honour an agreement he had signed to respect its decisions.
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"The only reason for my resignation is the national interest of my country so now Dr Abdullah should end his boycott and...And should respect the code of conduct that he had signed with the commission on the first day."
Abdullah is running against Ashraf Ghani Ahmadzai in the race to replace President Hamid Karzai, who is constitutionally barred from seeking a third term.
The standoff has upended the process after the Afghans received praise for a relatively smooth first round of voting on April 5, when millions of voters defied a Taliban threat of violence and cast their ballots.