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

The United Nations-backed agency responsible for investigating the results of the Afghan presidential election has invalidated ballots from thousands of polling stations, potentially pushing the country closer to a run-off vote.

The outcome of the two-month investigation by the Electoral Complaints Commission (ECC) focused on the rigging of ballot boxes and found "clear and convincing evidence of fraud relating to improperly recorded vote totals for candidates," according to a statement released Monday.

In a report on the Aug. 20 vote, the ECC confirms fraud occurred at more than 3,000 polling stations. It ordered that all the ballots at 210 of those polling stations be invalidated, which will eliminate thousands of ballots from the final count. Some voting stations showed fraud on up to 96 per cent of the ballots, according to the commission's report.

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Electoral Complaints Commission head Grant Kippen speaks at a news conference in Kabul on Monday. ((Omar Sobhani/Reuters))

As part of the audit and recount process, the UN commission also ordered the Afghan electoral authority, the Independent Election Commission (IEC), to invalidate a certain percentage of each candidate's votes.

A full recount would take a considerable amount of time, so the investigation has been based on a sampling, the report said.

The commission did not release updated result tallies on Monday, but according to several accounts, the findings of the five-member investigative panel will force a run-off vote. Ballot papers have reportedly been printed and plans drawn up to hold a run-off election by early November.

If enough votes for President Hamid Karzai were thrown out, his totals could drop below the 50 per cent threshold needed to avoid a second-round vote with his top challenger, former foreign minister Abdullah Abdullah.

Preliminary results from the election indicated Karzai won 54.6 per cent of the vote, enough to win outright without the need for a run-off. Abdullah won 27.8 per cent of the vote.

NATO pressures Karzai

NATO allies, including Canada, are pressuring Karzai to accept either a run-off election or a power-sharing government with Abdullah.

The West believes the formation of a government accepted by the Afghan people is crucial to combat the growing Taliban insurgency in the war-torn country and likely wants to avoid a run-off vote, said former Canadian foreign affairs minister John Manley.

Manley served as an international observer during the Afghan election.

Prime Minister Stephen Harper called Karzai on Monday and "urged President Karzai to maintain an unqualified commitment to the constitutional democratic process in Afghanistan," Harper's spokesman, Dimitri Soudas, said in an email.

U.S. Secretary of State Hillary Rodham Clinton said she, too, had spoken to Karzai several times in the past few days. According to Clinton, Karzai said he would announce his intentions Tuesday.

UN Secretary General Ban Ki-moon spoke with Karzai on Monday morning and was assured by the president that he would "fully respect" the constitutional process even if it means a second ballot, an agency spokeswoman said.    

Afghan commission must accept orders

Before any run-off election can be held, the Afghan electoral commission must first accept Monday's findings and would then be responsible for releasing a final tally and calling a second-round vote if necessary. But there have been reports the IEC — which is dominated by Karzai allies — will contest the data from the investigation.

Abdullah's campaign said that based on their examination of Monday's report, Karzai's share of the vote will be reduced to about 48 per cent.

"This is a step forward, now it is up to the IEC to announce the final results," said campaign spokesman Fazel Sancharaki.

Sancharaki said the IEC refusing to accept the report's findings would amount to an "illegal action."

Abdullah's camp has alleged the president is urging the Afghan election commission not to accept the results of the fraud probe.

The head of the ECC, Canadian Grant Kippen, told CBC News on Monday that he believes the results of the investigation will be accepted. "It's clear in the law that … they must in order to certify the final results take those orders into consideration and make the necessary adjustments," Kippen said.

Unclear future

Karzai's campaign declined to comment on the results of the investigation. The president has previously acknowledged irregularities in the election but has defended the process as "good and fair and worthy of praise, not scorn."

It is not clear what will happen if the Afghan electoral commission rejects the findings of the UN-backed panel or if Karzai were to refuse to participate in a run-off.

Officials familiar with the situation have told reporters that meetings between Karzai and Abdullah's campaigns and international representatives over the weekend explored a range of scenarios, including a power-sharing deal with Abdullah. Meetings were reportedly continuing on Monday.

With files from The Associated Press