The Aug. 20 poll has been increasingly marred by reports of ballot-box stuffing and suspicious tallies. A U.S. monitoring group has said "large numbers of polling stations" had more than 100 percent turnout and President Hamid Karzai's top challenger has accused him of "state-engineered" fraud.
All ballots from five polling stations in Paktika province should be voided because they show clear evidence of fraud, the Electoral Complaints Commission said in a statement. This is a more severe step than ordering a recount, in which the votes could eventually be included.
Decisions by the commission are final under Afghanistan's electoral law. The group is releasing decisions from each province as investigations finish.
International censure of the vote has increased since Tuesday, when election officials released preliminary results from 92 percent of polling stations showing Karzai had finally passed the 50 percent threshold needed to avoid a runoff. The voiding of ballots Thursday could change these results.
The complaints commission ordered an audit and recount countrywide of stations where turnout was at or above 100 percent, or where one candidate won more than 95 percent of the vote.
The Washington, D.C.-based National Democratic Institute said its analysis of results found large numbers of stations with more than 600 votes - the 100 percent mark - in Nuristan, Paktia, Helmand and Badghis provinces, along with others.
These are areas considered some of the least secure on polling day and in which anecdotal accounts of nearly empty polling stations suggested low voter turnout. Few international observers went to these areas because of security risks.
Though there are no official turnout figures from the Aug. 20 poll, government officials and independent observers have generally said voters showed up only in low numbers because of Taliban threats ahead of the vote and attacks on election day.
Dozens of people were killed amid rocket bombardments, bombings and polling station raids.
The monitoring group said it had "deep concern" over the high levels of fraud complaints pouring in. The Electoral Complaints Commission has received more than 2,800 complaints about polling day and the counting process, of which 726 have been deemed serious and specific enough to affect polling station results.
"It will be impossible to determine the will of the Afghan people," unless fraud complaints are thoroughly investigated, it said in a statement.
The group had more than 100 international and Afghan observers in 19 of Afghanistan's 34 provinces. It did not have observers in many of the provinces where it saw problems in the results, but the figures have been posted on the Web.
Partial results released so far show, far ahead of top challenger Abdullah Abdullah, who has 28 percent. Election officials have said they expect to release full results Saturday, but these will not be deemed official until all fraud complaints have been investigated and any re-counts are finished.
Election officials have said they are holding back suspicious results, but they appear to be using a different metric than the complaints commission because voting center results in which candidates won more than 95 percent of the vote have been posted, along with stations that have tallies higher than 600.
The National Democratic Institute says it is a nonpartisan organization aimed at strengthening democratic institutions. It is funded partly by private donations and the U.S. and other governments.