Hamid Karzai was declared Afghanistan's first directly elected president on Wednesday, report agencies.

"Karzai is the winner," declared Sultan Baheen of the United Nations-Afghan Joint Electoral Management Body which oversaw the October 9 elections.

Interim President Karzai won 55.4 per cent of the votes, 39 per cent higher than his nearest rival Yunus Qanooni, and enough to avoid a second round of voting.

Though Karzai's win was expected, the counting took time and the election commission had to wait for a report from an expert panel investigating allegations of fraud and irregularities on voting day.

The victory was announced soon after the UN-appointed panel concluded that the "shortcomings" on election day, including the low-quality ink, did not affect the ballot's outcome and were too minor to overturn Karzai's victory.

"There were shortcomings ... but they could not have materially affected the overall result," the panel's report said.