Al Jazeera's James Bays, reporting from Kabul, said if the IEC results were to stand, there would be no run-off and Karzai would be returned as president.
"But things are not that simple," he said.
Bays said: "We've had the Election Complaints Commission come out, saying they have clear and convincing evidence of fraud in these elections.
"They point to three provinces where they have particular concerns and they have launched a wide ranging order - anywhere nationwide ... where there was a 100 per cent turnout, they want a recount and an audit of everything that was in the ballot box.
"And also where one candidate has got more than 95 per cent of the vote, they want a recount and an audit.
"They want to look at all these ballots again, look at the handwriting, make sure for example that they were not written by the same person."
The commission said it would set aside results from 600 polling stations where it suspected irregularities.
Owing to mounting allegations of fraud, the IEC has excluded around 200,000 votes from 447 polling stations from preliminary results to be announced later this week, Daoud Ali Najafi, IEC chief electoral officer, told German Press Agency dpa.
The votes were suspicious and were sent to the ECC for adjudication, Najafi said, adding: "The ECC will decide if they would throw it out of the final result."
The ECC also ordered the IEC to recount votes from polling stations where more than 600 votes were cast - the most that could be cast at a single station.
The August 20 election was Afghanistan's only second direct presidential election, and has been overshadowed by claims of massive fraud.
The US, which has troops stationed across the country as part of its effort to defeat fighters allied to Taliban and al-Qaeda, said that the full result of the Afghan election could take weeks or months to emerge.
"It is very important that these elections are seen as legitimate in the eyes of the Afghan people, in the eyes of the international community. And I am not going to prejudge where this whole thing comes out," Ian Kelly, a spokesman for the US state department, said on Tuesday.
"It is not going to be a matter of days or weeks, it could be a matter of months to sort out all of these allegations."