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Zekria Barakzai, deputy head of the IEC, urged patience.
"We cannot confirm any claims by campaigning managers. It's the job of the election commission to declare the results. They should be patient," Barakzai said.
Dawood Ali Najafi, another IEC official, said it was too early to say whether there would be a run-off because not all results had been received from Afghanistan's 34 provinces.
An independent Afghan monitoring body, FEFA, said it was concerned about the quality of the poll after receiving reports from its observers across the country of fraud and interference.
Barakzai said two convoys of election workers transporting ballot boxes had been attacked following the vote. In one case, in Balkh province in the north, an election worker was killed and ballots that had already been counted were burned.
He said preliminary figures showed overall turnout was around 40-50 percent. This would be roughly in line with estimates by Western diplomats before the poll.
Much is likely to depend on turnout in southern areas, such as Karzai's home province of Kandahar, where the president draws his strongest support but where voters faced the brunt of Taliban attacks and intimidation.
Abdullah's spokesman, Fazl Sangcharaki, said the north had voted solidly for Abdullah, except in Jowzjan province, home of Uzbek militia chieftain Abdul Rashid Dostum, who returned to the country days before the vote to campaign for Karzai.
Western backers have expressed concern about Karzai's tactic of seeking support from former militia chiefs, afraid that deals made to secure votes could bring warlords back to power.
In Washington, President Barack Obama hailed the conduct of the election and vowed to press on with his strategy, which has involved sending thousands of additional troops to the country.
"We have to focus on finishing the job in Afghanistan but it is going to take some time," Obama said from the White House.
The election was a test for Obama's new strategy aimed at reversing Taliban gains. U.S. combat casualties have risen amid a U.S. troop buildup and opinion polls have shown weakening American backing for the war.
(Writing by Paul Tait; Editing by Alex Richardson)