An observer for Afghan President Hamid Karzai watches election workers entering data into a computer at the election result tally centre in Kabul on Tuesday. (Manish Swarup/Associated Press)

The ballots from several polling stations in Afghanistan's presidential election will be excluded from the final tally, the UN-backed commission investigating fraud said.

The Electoral Complaints Commission (ECC) announced on Thursday that the first orders have been issued to exclude some ballots from the presidential vote, which has become increasingly marred by reports of fraud.

Nearly all the ballots come from 51 polling stations in Kandahar province, five polling stations in Paktika province and 27 in Ghazni province. They are being excluded from the final tally, the commission said, because they show "clear and convincing evidence of fraud."

The commission began investigating the ballots cast at those polling stations after several complaints about the polling and counting period.

"During investigation the ECC found a number of indicators of fraud including unfolded ballots, votes for candidates inserted inside bundles for other candidates, miscounted ballots, missing material, uniformity of markings, seal numbers which did not match numbers on the record of seals and lists of voters with numerous fictitious card numbers," said the ECC's written statement.

No estimate has been provided regarding how many ballots will be annulled by the decision.

Severe step

Excluding the votes is a more severe step than ordering a recount, where the votes could have been included.

An Afghan cycles past an election poster for Afghanistan President Hamid Karzai in Kabul on Tuesday. (Farzana Wahidy/Associated Press)

Decisions made by the commission — composed of three international members appointed by the UN and two Afghans — are final under Afghanistan's electoral law.

There have been increasing reports of ballot-box stuffing and suspicious tallies.

The commission has received more than 2,800 complaints about polling day and the counting process, of which 726 have been deemed serious and specific enough to affect polling station results.

The group had already ordered an audit and recount countrywide of stations where turnout was at or above 100 per cent and where one candidate won more than 95 per cent of the vote.

The National Democratic Institute, a U.S. monitoring group, reported on Thursday its analysis shows a "large number of polling stations" in the provinces of Nuristan, Paktia, Helmand and Badghis had more than 100 per cent turnout in the Aug. 20 vote.

"Unless the clear and convincing evidence of fraud found by the ECC is addressed, it will be impossible to determine the will of the Afghan people," the National Democratic Institute said in a written statement.

Karzai in lead

The most recently released figures show that President Hamid Karzai has 54.1 per cent of the vote with almost 92 per cent of ballots counted.

Officials have said the complete results of the vote are expected to be ready on Saturday, but they will not be official until all fraud complaints have been investigated.

The investigation and the ordered recounts could mean it will be months before a winner is declared, officials have said.

If enough votes are thrown out, Karzai could lose the majority that preliminary results are showing and force him into a run-off vote with the top challenger, former foreign minister Abdullah Abdullah.

Abdullah, who holds 28.3 per cent of the vote, has accused Karzai of "state-engineered" fraud.

All three provinces where votes have been thrown out by the commission are dominated by ethnic Pashtuns and are areas where Karzai, also an ethnic Pashtun, would expect to do well.

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."

Meanwhile Karzai has praised election officials for carrying out the vote with "honesty and impartiality."

With files from The Associated Press