Ahmadzai 'leads Afghanistan poll'
His rival Abdullah Abdullah has alleged the vote was marred by massive fraud and said he will not accept any results until an investigation into the allegations is completed.
In a news conference, commission chairman Ahmad Yousuf Nouristani said Mr Ahmadzai took 56.44% of the vote, while Mr Abdullah was behind with 43.56%.
The Independent Election Commission acknowledged that vote-rigging had occurred and promised to launch a more extensive investigation before final results are released.
"We cannot ignore that there were technical problems and fraud that took place during the election process," the Mr Nouristani said.
"We are not denying fraud in the election, some governors and Afghan government officials were involved in fraud."
The results showed that Mr Ahmadzai had about 4.5 million votes while Mr Abdullah had 3.5 million, he said.
Mr Abdullah, a former foreign minister who won the first round of voting on April 5 by a large margin, says his campaign monitors recorded ballot box stuffing and other irregularities, prompting him to suspend his cooperation with electoral officials.
The European Union also expressed concern about "highly worrying indications of potentially widespread fraud".
The preliminary results had been due on July 2 but were delayed by five days while officials said they would audit ballots from nearly 2,000 polling stations that had at least 599 votes.
Mr Abdullah said that was insufficient and demanded the results be postponed until all fraud allegations were resolved.
The impasse has threatened to undermine what the US and its allies had hoped would be the country's first democratic transfer of authority after President Hamid Karzai agreed to step down after two terms as legally required.
Western officials were looking for a smooth transition to show progress ahead of the withdrawal of US and allied combat troops by the end of this year. Whoever wins will inherit an impoverished country mired in insurgency and facing high unemployment and declining foreign aid.
Both candidates have promised to sign a security pact with the US that would allow nearly 10,000 American forces to remain in the country in a training capacity and to conduct counter-terrorism operations.
A disruption in the announcement of election results could mean another delay in finalising that agreement, which was rebuffed by Mr Karzai.
Mr Ahmadzai, a former finance minister and World Bank official, also filed complaints of irregularities in the June 14 balloting but has insisted that the agreed-upon counting process be respected and said any further delays in releasing results would be unacceptable.
According to the election commission's official timetable, final results are due on July 22. Mr Karzai has set August 2 as the date for the new president to be inaugurated.
The campaign teams, meanwhile, were holding technical and political talks in a bid to resolve the crisis, although both candidates have ruled out a deal on a coalition government.