Afghan President Hamid Karzai, right, talks with UN assistance mission head Kai Eide of Norway, left, and U.S. Senator John Kerry after announcing he was endorsing a Nov. 7 run-off vote in the country's presidential election. (Musadeq Sadeq/Associated Press)

International leaders welcomed Afghan President Hamid Karzai's acceptance of a run-off vote but said there were still challenges to overcome in making Afghanistan's electoral process fair.

U.S. President Barack Obama called Karzai's acceptance of the findings of Afghanistan's Independent Election Commission a key step in "a credible process" for the people of Afghanistan.

Prime Minister Stephen Harper said while the first round of elections was not without controversy, the government was pleased that both candidates recognized the "need for a run-off election in the best interests of Afghan democracy."

"Canada has consistently stated that all parties must respect the Afghan electoral process and the Afghan constitution," Harper said in a statement.

An election worker carries a ballot box at an election commission office in Jalalabad, Nangarhar province, east of Kabul on Aug. 25. (Rahmat Gul/Associated Press)

He encouraged Afghans to vote in the second round of elections. Some have said they feared a flare-up of violence and were wary of voting again.

The IEC ordered a Nov. 7 run-off vote in the presidential election between Karzai and opponent Abdullah Abdullah after investigators determined Karzai did not earn enough valid votes for a majority. Afghan electoral law states a run-off is required if no candidate gets above 50 per cent of the vote.

The chairman of the IEC, Azizullah Lodin, said the commission did not want to "leave the people of Afghanistan in uncertainty" any longer.

UN panel found evidence of massive fraud

UN Secretary-General Ban Ki-moon said Tuesday that organizing a second election would be a "huge challenge" but that the UN would do everything it could to make sure the election was transparent and credible.

Jawed Ludin, Afghanistan's Ambassador to Canada, said the run-off election will not be easy but said it is necesary.

"Democracy is taking roots, and everything we do — the international community, Afghans — it's going to affect how this foundation is laid," he told CBC News.

The findings come after the UN-backed Electoral Complaints Commission (ECC) invalidated ballots from thousands of polling stations.

The original vote count gave Karzai 54.6 per cent of the total, enough to win outright against his nearest challenger, former foreign minister Abdullah.

Canadian Grant Kippen of Ottawa, who heads the UN commission, said Monday that investigators found a significant amount of fraud in the results sample they looked at.

Karzai bows to international pressure

Karzai was facing considerable international pressure to abide by the finding of the ECC and agree to either a run-off or a power-sharing arrangement with Abdullah.

Much of the pressure was coming from representatives of the United States, Canada and Britain, three countries with troops stationed in Afghanistan and fighting alongside his government.

Standing alongside Karzai when he made the announcement was U.S. Senator John Kerry, the chair of the U.S. Senate foreign relations committee, who had frequently visited Karzai to address U.S. concerns over the legitimacy of the election.

Kerry said Karzai "has shown genuine leadership in the decision he has made today" and said the agreement had turned the crisis into a "moment of great opportunity."

One option to avoid a run-off was a power-sharing deal, though the form it would take is unclear. It could also take weeks or months to hammer out an agreement between the two rivals.

Karzai ruled out a coalition government, telling reporters "there is no space for a coalition government in the law."

A spokesman for Abdullah said the former foreign minister still sees a second-round vote as the best option. However he also said that should a run-off vote not be possible, due to weather or security concerns, Abdullah would be open to a power-sharing arrangement with Karzai.

A report released Monday by the ECC confirmed that fraud occurred at more than 3,000 polling stations. It ordered that all the ballots at 210 of those stations be invalidated. Some voting stations showed fraud on up to 96 per cent of the ballots, according to the commission's report.

With files from The Canadian Press and The Associated Press