Opposition candidates say some ballot boxes have been filled with fake votes
Election complaints officials in Afghanistan say they are looking into more than 560 major allegations of fraud from the 20 August vote.
The tally doubles the figure of serious allegations reported two days ago.
Full preliminary results are due next week, but the final results will not be made official until major fraud allegations are investigated.
The latest partial results give President Hamid Karzai 46% of the votes compared to Abdullah Abdullah's 31.4%.
A candidate needs 50% of votes cast to avoid a second round run-off which, if needed, would be held in October.
The independent Electoral Complaints Commission said on Sunday that of more than 2,000 allegations of fraud and intimidation during voting and vote-counting, 567 had been deemed serious enough to affect the election's outcome, if proven.
President Karzai rejects allegations of state-crafted fraud
On Friday, the commission had reported 270 major allegations.
With two-thirds of polling stations still to announce their results, Mr Abdullah has already alleged "massive, state-crafted" fraud.
He told the BBC on Saturday that ballot boxes had been stuffed with hundreds of thousands of votes.
"My concern is about massive fraud, state-crafted, state-engineered fraud which has taken place throughout the country," he said.
Mr Karzai has rejected allegations of state-crafted fraud.
His comments came days after it emerged that US special envoy to Afghanistan Richard Holbrooke, in a meeting with Mr Karzai, raised concerns about ballot-stuffing and fraud by a number of candidates' teams.
However, officials of both Mr Holbrooke and Mr Karzai denied reports their talks had been "explosive" and a "dramatic bust-up."
With the election commission saying just over two million votes had now been counted, Kabul lawmaker Ramazan Bashardost was placed in third position, ahead of former World Bank economist Ashraf Ghani.