The election has been dogged by allegations of irregularities and fraud
The head of the UN mission in Afghanistan has admitted his deputy left the country after a row between them over the disputed Afghan election.
But Kai Eide, a Norwegian diplomat, denied reports that he had ordered his US deputy, Peter Galbraith, to leave.
EU election observers have meanwhile said that about 1.5m votes - about a quarter of all ballots - cast in the presidential vote could be fraudulent.
They say that 1.1 million votes cast for President Karzai are suspicious.
EU observers say they also have doubts about 300,000 cast for his main rival, Abdullah Abdullah - along with a number of votes for other candidates.
The BBC's Martin Patience in Kabul says that the latest fraud allegations are the most serious to be made so far suggesting that up to a quarter of all votes are suspicious.
Our correspondent says the allegations could have major implications for the outcome of the election and could put pressure on the Afghan Electoral Complaints Commission to widen its investigation into voter fraud.
Remaining preliminary results are due to be released on Wednesday, four weeks after the election, although the final declaration of a winner is not likely to be made for some weeks.
Mr Eide and Mr Galbraith reportedly disagreed over the extent to which vote recounts were necessary.
AFGHAN POLL FRAUD
15 Sep: ECC chief says 10% of votes need to be recounted
8 Sep: Poll complaints body orders some recounts nationwide
8 Sep: IEC says votes from 600 polling stations "quarantined"
3 Sep: Claims 30,000 fraudulent votes cast for Karzai in Kandahar
30 Aug: 2,000 fraud allegations are probed; 600 deemed serious
20 Aug: Election day and claims 80,000 ballots were filled out fraudulently for Karzai in Ghazni
18 Aug: Ballot cards sold openly and voter bribes offered
The row centres on how to deal with alleged election fraud, with Mr Galbraith reportedly advocating a wholesale recount of last month's poll. Such a recount would probably mean a second-round run-off, potentially leaving Afghanistan in political limbo for months.
"There has been a disagreement," Mr Eide told the BBC's Newshour programme on Tuesday.
"That disagreement has been resolved through his [Mr Galbraith's] proposal to leave the mission for a while and then he'll come back.
"He's a valuable deputy and I do hope that we can re-establish a good team and work together."
Mr Eide declined to talk about details of his disagreement with Mr Galbraith.
But he said it was important for the UN to respect the constitutional bodies in charge of the presidential election "to avoid any impression that there is foreign interference".
The EU observers did not give an estimated turnout figure, but it is expected to be low - mostly because of Taliban intimidation of voters.
President Karzai is leading the count with 54.3% of the disputed votes. Mr Abdullah is estimated to have 28.1% of the vote.
Analysts say that turnout is around 30-35%, not much higher than six million out of a total registered electorate of 17 million.