ECC officials have already invalidated ballots from three provinces
Ballots from 10% of polling stations in Afghanistan's presidential vote need to be recounted because of indications of fraud, a top election official says.
About 2,500 polling stations across the country were affected, Grant Kippen of the UN-backed Electoral Complaints Commission (ECC) said.
His comments come amid reports of serious tensions within the UN mission over the issue of electoral fraud.
A substantive vote recount could force incumbent Hamid Karzai into a run-off.
With 95% of the vote counted, Mr Karzai had a 54% share, electoral officials said on Saturday.
But if fraud investigations cause this figure to drop below 50%, he and closest challenger Abdullah Abdullah, who has 28% of the vote, would have to go to a second-round vote.
Afghanistan's second direct presidential election on 20 August was marred by widespread claims of vote-rigging and intimidation.
Martin Patience, BBC Kabul correspondent
The recount is actually more of an investigation. Officials will be sifting through the votes looking for obvious signs of fraud such as uniform markings, the way the ballots are folded and even the way they've been stamped.
It's a process expected to last for weeks. If because of a recount, President Karzai doesn't have an outright majority, he will need to face a second round.
And that will bring another set of headaches. When would a second round be held? Because of the harsh winter here - it may have to be postponed until next spring.
With this election beset by problems, why would it be any different a second time round?
The ECC last week ordered Afghanistan's Independent Election Commission to identify stations reporting 100% turn-out or where one candidate received more than 95% of the vote in order for recounts to be carried out.
"About 2,500 plus polling stations are affected by the order and all provinces are affected," ECC Chairman Grant Kippen told AFP news agency.
Last week the ECC invalidated ballots from dozens of polling stations in the three provinces of Paktika, Kandahar and Ghazni.
Correspondents say that investigations into possible fraud could take weeks, if not months.
No official announcement on who has won the election can be made until those investigations are complete.
Mr Kippen's remarks come amid reports of deep divisions among UN diplomats in Kabul over how to proceed in the wake of the election.
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 Times reports that the head of the UN mission, Kai Eide, ordered US representative Peter Galbraith out of Afghanistan after the two reportedly disagreed over the extent to which vote recounts were necessary.
A wholesale recount as advocated by Mr Galbraith would be likely to ensure a second round run-off was held, the newspaper reported.
But Mr Eide feared such a run-off could be delayed until May, potentially leaving Afghanistan in political limbo, The Times said.
The BBC understands Mr Galbraith has been advised to have a "cooling off" period in New York - but he is expected to be joined by Mr Eide in a couple of weeks when they are to brief the UN Security Council.
Both men are then expected to return to Kabul, with Mr Galbraith remaining in his current position.
There has been no formal comment from the UN mission.