The audit is aimed at reversing a destabilising political crisis that has threatened to widen the country's ethnic fissures as foreign troops prepare to withdraw after more than a decade of war.
Some 23,000 ballot boxes are being transported by the Afghan army and NATO forces to the capital, where they will be examined at 100 verification stations.
"The audit will take two to three weeks, we are planning to form hundreds of teams for this audit," Ahmad Yousuf Nuristani, chief of the Independent Election Commission told a press conference.
The move was agreed upon by the two rival presidential contenders, Abdullah Abdullah and Ashraf Ghani, following a deal brokered by US Secretary of State John Kerry.
US President Barack Obama today hailed the "courage" of the two candidates, as well as Kerry's efforts in breaking the deadlock.
"This progress will honour both candidates who have put the interests of a united Afghanistan first, the millions of Afghans who defied threats in order to vote, and the service of our troops and civilians who have sacrificed so much," he said in a statement from the White House.
"Both teams have agreed for the thorough and serious audit of the votes, and we firmly stand on our commitment to the people that the clean votes will be separated from the unclean ones," he said.
The impasse over the vote to succeed President Hamid Karzai has raised fears of a return to the ethnic violence of the 1990s.
Abdullah -- who says he already suffered one stolen election at Karzai's hands in 2009 -- is half-Tajik while Ghani is from the majority Pashtun community, as are the Taliban.
NATO's International Security Assistance Force (ISAF) -- whose main Kabul compound lies next to the civilian airport -- is providing air transport for some 40 per cent of the votes.
The deal followed weeks of fruitless diplomatic efforts and paves the way for a government of national unity, including a role for the losing side.
Auditing began just hours after Afghan security officials put an end to a Taliban siege of Kabul's airport in the militants' latest attempt to steal the initiative amid the power struggle.
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