Former Afghan Finance Minister Ashraf Ghani is leading the race to replace Hamid Karzai as president, according to preliminary results.
Mr Ghani won 56.44% of votes in the 14 June run-off, election officials said. His rival Abdullah Abdullah had 43.56%.
Mr Abdullah, who fell just short of an outright majority in the first round, rejected the result.
Both men have alleged fraud in the election. Votes are being re-checked at more than 7,000 polling stations.
They represent nearly a third of centres where votes were cast and correspondents say recounts could significantly alter the result.
‘Only initial results’
Chief election commissioner Ahmad Yusuf Nuristani stressed that the results were not final and acknowledged that there had been “some mistakes in the overall process”.
“It is only initial results,” he told a news conference in Kabul. “There is a chance of change in the overall figure.
“The announcement of preliminary results does not mean that the leading candidate is the winner.
“We announced preliminary results today and it is now the complaints commission’s duty to inspect this case.”
The election commission said it would now audit an estimated four million votes.
Final results are due on 22 July.
Mr Abdullah was well ahead after the first round in April, winning 45% of votes cast while Mr Ghani had 31.5% and came second.
Correspondents say the election could pose worrying questions for future stability if the final outcome is not accepted.
Ghani, a former World Bank official, is believed to have won votes among tribes from the Pashtun majority in southern and eastern areas.
A spokesman for Mr Abdullah, who is of Tajik-Pashtun parentage, was swift to reject Monday’s initial figures.
“As we had rejected the outcome of the result before and had declared that we could not trust the election commission, our stand is the same today,” spokesman Fazlurrahman Oria told the BBC.
The two rival camps were locked in talks for much of Monday, delaying the results announcement as they sought to defuse tensions over the vote.
It comes during a critical year for Afghanistan. Most foreign troops are due to withdraw by the end of 2014.
Afghanistan’s 2009 presidential election was also marred by claims of mass fraud. Dr Abdullah pulled out of the race, which was won by Mr Karzai.