The election complaints commission has said it is investigating 225 allegations of misconduct, far fewer than the number alleged by Abdullah.
Grant Kippen, a Canadian who heads the commission, said that while there were "significant complaints", none were specifically directed at individual candidates.
Just a day earlier, Abdullah accused Karzai of rigging the polls, saying that the president "uses the state apparatus in order to rig an election".
"This is under his leadership that all these things are happening, and all those people which are responsible for this fraud in parts of the country are appointed by him," Abdullah said in an interview with The Associated Press.
An aide to Karzai dismissed the claims.
"These are not new allegations. These were made even before the election took place," Waheed Omar, Karzai's campaign spokesman, said.
He said that Karzai's camp had filed complaints about Abdullah's team with the electoral complaints comission, an election watchdog made up of both Afghan and international members.
"We have documented violations that were made by Abdullah's campaign team," Omar said.
"But we believe our job is to report to the elections complaint commission ... We do not want to make a media propaganda campaign out of the violations we have documented."
The commission, which acts effectively as a court of appeal to Afghanistan's own Independent Election Commission (IEC), said that of the 225 complaints it was investigating, 150 were "priority" complaints.
It described another 35 as "high priority".
James Bays, Al Jazeera's correspondent in Kabul, said: "We have [heard] complaints of intimidation, fraud, and of the IEC staff not doing their jobs properly - possible misconduct by them."
The commission vowed its investigation would not hold up the release of election results, preliminary figures for which are due on Tuesday, with the official tally expected in September.
Afghan's voted on August 20 for a new president and 420 councillors across 34 provinces, although violence and Taliban threats kept voter turnout low.
The contest was thought to have come down to Karzai and Abdullah, both of whom initially claimed victory and in recent days have begun preparing for a possible runoff, likely to be held in October.
Under Afghanistan's election system a presidential candidate must win over 50 per cent of the vote.
Bays said: "Most people are saying that if the election isn't rigged - if there isn't fraud - then it is likely that there could well be a second round."
Despite the allegations of vote rigging, and attacks on election day that left at least 26 people dead, Afghan and Western officials were relieved that Taliban fighters did not succeed in their threat to derail the elections.
European Union monitors were quick to call the vote "good and fair", a move criticised by others as premature since election results had yet to be released.