The result of the 9 October poll, the country's first presidential election, might not be out until early November due to the logistics of taking ballot boxes from remote areas in Afghanistan's mountains and deserts to counting centres.
But with almost 12% of the ballot counted so far, Karzai is comfortably in front. His main rival, Yunis Qanuni, said the vote was always loaded in Karzai's favour.
"There was cheating before the election, there was cheating during the election and it is still continuing," the former education minister said on Monday.
"The newborn baby of democracy was slaughtered in front of our nation and the international community on the day of its birth."
Despite his allegations of fraud, Qanuni - from the country's Tajik minority - promised to help Karzai, a member of the Pashtun community which is the largest in Afghanistan, stabilise and rebuild a country shattered by war and riven by ethnic divides.
"If my previous friend, Mr Karzai, is successful ... I will congratulate him and help him reconstruct and forge national unity in a new Afghanistan," he said.
Karzai's rivals had threatened to refuse to recognise the results until the election commission established a three-member panel to investigate voter fraud.
Soon after meetings with US ambassador Zalmay Khalilzad in the days after the election, Qanuni and two other contenders from the main ethnic minorities all said they would honour the outcome as long as the panel did its job.
Hamid Karzai has gained 60%
of votes counted thus far
Karzai was installed in office after US forces overthrew the Taliban regime three years ago for harbouring Usama bin Ladin.
Karzai has garnered just over 60% of the votes counted so far, remaining on course to score above the 51% mark needed for an outright win without going to a November runoff against his nearest rival.
Qanuni was in second place with nearly 19%.
General Abd al-Rashid Dustum, an ethnic Uzbek from the north, had 10%.
None of the other 15 candidates managed double-figure results.