Whoever wins will lead the country as it undergoes a major transition from rule by President Hamid Karzai, the only leader it has known since the 2001 U.S.-led invasion that ousted the Taliban. He also will face a strong challenge to end violence and improve the economy despite a resilient Taliban insurgency and declining foreign aid. Both candidates have promised to sign a security pact with the Obama administration that would allow nearly 10,000 American forces to remain in the country in a training capacity and to conduct counterterrorism operations. A disruption in the announcement of election results could mean another delay in finalizing that agreement, which was rebuffed by Karzai.
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, claiming the electoral official helped engineer the vote-rigging.
Abdullah received news of Amarkhail's resignation as he was holding a news conference.
"The door is now open for us to talk to the commission and talk about the conditions and circumstances that will help the process," he said. "We do believe in transparency of the process and we will defend the legitimacy of the process."
Western officials have long said they anticipated irregularities and the determining factor would be whether the vote rigging was sufficient to affect the overall outcome. The 2009 re-election of Karzai was marred by widespread ballot box stuffing and proxy voting, leading Abdullah, who was runner-up at the time, to refuse to participate in the runoff.
Abdullah won the first round but failed to gain the majority needed to avoid a runoff. He raised his allegations before any results were released, saying he had to act pre-emptively because reports by some 50,000 campaign monitors deployed at the polls showed Ahmadzai coming from behind with an unrealistic lead.
Amarkhail defended the conduct of the vote and called on Abdullah to resume relations with the Independent Election Commission and honor an agreement to respect its decisions.
"I want to say that there has not been any pressure on me to resign," he said at a news conference. "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."
According to the election commission's official timetable, preliminary results are due on July 2, and final results on July 23. Karzai has set Aug. 2 as the date for the new president to be inaugurated.
In a statement, the U.N. mission in Afghanistan called Amarkhail's resignation "a step that helps protect Afghanistan's historic political transition and contributes to an orderly and timely electoral process under the country's legal and institutional framework and through its mandated electoral institutions and their procedures."
It also urged both candidates "to fully re-enter the electoral process, cooperate with the electoral institutions and respect their decisions."
Western officials are looking for successful elections to show progress in the country, which has been torn by decades of conflict. Karzai is constitutionally barred from seeking a third term. The Taliban threatened a campaign of violence to disrupt the balloting, but millions of voters still turned out to cast their ballots in both the first round on April 5 and the runoff vote.
As a result of complaints by both candidates, electoral officials are auditing 10 percent of the ballots cast in five provinces — Khost, Paktia, Paktika, Ghor and Nuristan — where fraud allegations were heaviest, Independent Election Commission chairman Ahmad Yousuf Nouristani said. He said national and international observers will be present. Officials would use that to determine how much of the vote in each province was expected, he said.
It was unclear what would happen if major fraud is confirmed. Abdullah has called for new elections in the contested areas, but the election law calls for the contested ballots to be thrown out.
Ahmadzai's spokesman Hamidullah Farooqi praised Amarkhail for what he called a brave decision.