The row came as the final preliminary result gave Mr Karzai victory with 54.6 percent on September 16. The result is not yet official.
EU election observers earlier said about 1.5m votes - about a quarter of all ballots - could be fraudulent. The claims came amid a growing strain in the international community about how to deal with the election fallout.
Although Wednesday's results announcement represents a complete tally of votes, the final declaration of a winner is not likely to be made for some weeks.
Earlier, the head of the UN mission in Afghanistan admitted his deputy had left the country after a row between them over the election. But Kai Eide, a Norwegian diplomat, denied reports he had ordered his US deputy, Peter Galbraith, to leave.
Also on Wednesday, US President Barack Obama said there was "no immediate decision pending" on sending more troops to tackle a mounting Taliban insurgency.
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