Of the over 1 million votes polled till Monday, Karzai led with nearly 62 per cent, while his nearest rival, Qanooni, had close to 20 per cent.
Uzbek General Abdul Rashid Dostum had about 10 per cent, while Hazara minority leader Haji Mohammad Mohaqiq had close to four percent. Masouda Jalal, the only female candidate, had just over one per cent.
Afghanistan elections: Who's Who
Over 12 million Afghans had registered to vote, including 850,000 refugee voters in Iran and Pakistan.
Owing to the difficult terrain, ballots have been collected from only 29 of Afghanistan's 34 provinces so far, and full results are not expected till the end of the month.
Most candidates boycott Afghan polls
Addressing a press conference Monday, Qanooni said he had evidence to prove that the ballot boxes were illegally stuffed with Karzai votes in four provinces: Ghazni, Herat, Zabul and Kunduz. His representatives were threatened as they went to check on suspected ballot-box stuffing in Zabul province, the former interior minister said.
Qanooni also claimed that his representatives were prevented from monitoring ballot boxes in transit from polling stations to the counting centers. Some boxes arrived at the counting centers with broken seals, he said.
"These violations and cheating were organized in advance," Qanooni said.
Claiming he had sent at least 30 written complaints to the UN-Afghan electoral commission about electoral fraud, he said: "If his excellency Mr. Karzai, my old friend, succeeds in a fair and transparent election, I will congratulate him and cooperate with him.
"But if the result is fraudulent, the legitimacy of this election will be in question."
But Sultan Baheen, a spokesman for the electoral commission, rejected Qanooni's allegations, saying the candidate's representatives refused to accompany ballot boxes brought from Iran and Pakistan.
"There is no indication of what the candidates are saying, that boxes have been emptied and refilled," Baheen added. "There's nothing like that."
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