Both presidential candidates claim to have won the June 14 election, triggering a political stalemate and rising ethnic tension as US-led NATO combat troops withdraw after 13 years of fighting the Taliban.
The United Nations has said the audit results should be finalised by September 10, with the delayed inauguration of President Hamid Karzai's successor scheduled to be held soon after.
But poll rivals Ashraf Ghani and Abdullah Abdullah have failed to come to an agreement on a national unity government, which was negotiated under a deal to save the country from slipping back into the ethnic division of the 1990s civil war.
"The auditing and recounting process of all the votes have been concluded," Noor Mohammad Noor, Independent Election Commission (IEC) spokesman, told reporters in Kabul.
The IEC will now compile results from the audited ballot boxes and decide which of the disputed votes should be thrown out, before a 72-hour window for appeals against its rulings.
About eight million votes were individually checked during the audit, with both campaigns arguing fiercely over alleged evidence of fraud.
The incoming president will also be under pressure to sign security deals with the US and NATO to ensure further support after the foreign troops' combat mission ends in December.
A NATO summit in Britain yesterday renewed funding for the Afghan security forces, who are struggling against a series of new Taliban offensives, but delegates urged the presidential candidates to end their stand-off.
Outgoing President Hamid Karzai decided not to travel to the summit, and Afghanistan was instead represented by Defence Minister Bismillah Khan Mohammadi.
