Of the 225 complaints it was investigating, the commission said at that 150 were "priority" complaints and described another 35 as "high priority".
Grant Kippen, a Canadian who heads the commission, said that while there were "significant complaints" of vote irregularities, none were specifically directed at individual candidates.
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 Hamid Karzai, the incumbent president, and Abdullah Abdullah, his former foreign minister and main challenger, both of whom had initially claimed victory.
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."
Both candidates have begun preparing for a possible runoff, likely to be held in October, but neither have held back in their allegations of misconduct.
Abdullah accused Karzai of using the state to "rig" the polls, the most direct accusations he has yet made against his rival.
"He uses the state apparatus in order to rig an election," Abdullah said in an interview with The Associated Press.
He went on to say that it "doesn't make the slightest difference" whether Karzai or his supporters ordered the alleged fraud.
"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.
"And I'm sure he has all those reports, so he knows all of this. This should have been stopped and could have been stopped by him."
Waheed Omar, Karzai's campaign spokesman, dismissed Abdullah's allegations and claimed the president's camp had submitted its own reports of fraud allegedly committed by Abdullah's followers.
"We do not want to make a media propaganda campaign out of the violations we have documented"
Karzai's campaign spokesman
"These are not new allegations. These were made even before the election took place," Omar said.
"We have documented violations that were made by Abdullah's campaign team. 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."
Omar said losing candidates often claim fraud to "try to justify their loss".
Despite the allegations, and attacks on election day that left at least 26 people dead, Afghan and Western officials were relived that the Taliban 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.