Afghans cycle past an election poster in Kabul on Tuesday. (Manish Swarup/Associated Press)

A UN-backed commission on Tuesday ordered a partial recount of tainted ballots in Afghanistan's presidential election after finding "clear and convincing evidence of fraud."

President Hamid Karzai has 54.1 per cent of the vote with almost 92 per cent of ballots counted in the country's presidential poll, but Afghanistan officials say recounting the votes could mean it would be several months before a winner is declared.

If Karzai wins a majority, he would avoid a run-off with top challenger Abdullah Abdullah, who has 28.3 per cent of the vote.

However, widespread allegations of ballot-box stuffing and suspicious tallies are casting doubt on the legitimacy of the Aug. 20 vote as the country awaits final results.

More than 720 major fraud charges have been lodged with the complaints commission.

Daoud Ali Najafi, chief electoral officer of the Afghan-run Independent Election Commission, which organized the vote, said recounting votes could take "two months or three months." Officially certified results were due by late September.

Afghanistan's population, estimated at 33 million, is about the same as Canada's.

Afghan presidential candidate and current President Hamid Karzai casts his vote at a polling station in Kabul on Aug. 20. (Rafiq Maqbool/Associated Press)

Grant Kippen, chair of the UN-backed Electoral Complaints Commission, said Tuesday it had identified questionable results in Ghazni, Paktika and Kandahar provinces in stations showing 100 per cent turnout or with a presidential candidate receiving more than 95 per cent of the vote.

"We went down and investigated various polling stations. We opened ballot boxes and saw evidence that ballots had been marked in uniform markings," Kippen told CBC News in an interview.

In some cases, people "had [an] extensive number of ballots in the ballot boxes," and in some cases, polling stations had more ballots returned than had been assigned to that area, he added.

"So based on that … we made the decision to exclude the ballots in those particular polling stations."

Officials have also reported dozens of voting sites where Karzai won rounded blocks of ballots — 200, 300 and 500 votes — results one official labelled "illogical."

Complaints from other provinces

The three provinces ordered to do recounts are in the southern part of the country, where support for Karzai is strongest. However, the commission is also probing other regions, said Kippen.

"This isn't the only part of the country where we've received complaints. We've had complaints actually from every province in the country."

The commission — comprised of three international members appointed by the UN and two Afghans —plans to visit other regions of the country in the next week to investigate other allegations of fraud, he added.

That will further delay release of the preliminary results, which had been due that Thursday, he said.

More than 650 major fraud charges have previously been lodged with the Independent Electoral Commission, which said results from 447 polling stations had been thrown out.

Daoud Ali Najafi, the commission's chief electoral officer, said that amounts to about 200,000 ballots.

He said the ballots have been sent to the UN commission, which will decide if any can eventually be included in the official count.

With files from The Associated Press