The Electoral Complaints Commission threw out ballots at 51 sites in Kandahar, 27 in Ghazni and five in Paktika. Ethnic Pashtuns dominate the three provinces, and President Hamid Karzai, who is an ethnic Pashtun, expect to do well there. The commission did not say how many votes were nullified, according to the Associated Press.
Preliminary results from 92 percent of the polling stations show Karzai has more than 54 percent of the vote count, far ahead of top challenger Abdullah Abdullah, who has 28.3 percent. If the commission throws out enough votes, however, Karzai could drop below 50 percent and be forced into a run-off.
The election, which took place Aug. 20, 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 Abdullah has accused Karzai of state-engineered fraud.
The Electoral Complaints Commission ordered an audit and recount of stations where turnout was at or above 100 percent, or where one candidate won more than 95 percent of the vote.
The commission received more than 2,800 complaints about the election, of which 726 have been deemed serious and specific enough to affect polling station results. Throwing out ballots is a more severe step than ordering a recount, in which the votes could eventually be included. The commission did, however, order some votes to be recounted in Ghazni.
Election officials said they expect to release full results Saturday, but these will not be deemed official until all fraud complaints have been investigated and any recounts are completed. That process could take weeks or even months.
In a statement, the ECC said that its investigations in Ghazni found "a number of indicators of fraud," including unfolded ballots, votes for candidates inserted inside bundles for other candidates, miscounted ballots, missing material, uniformity of markings, seal numbers that did not match numbers on the record of seals and lists of voters with numerous fictitious card numbers, the BBC reported.
The ECC added that "ballots were not legally cast, or were not legally counted" in Kandahar and Paktika.
Under Afghan elections law, decisions by the commission are final. The group is releasing decisions from each province as investigations finish. The commission comprises one American, one Canadian, one Dutch and two Afghans.
The Washington, D.C.-based National Democratic Institute, a nonpartisan organization aimed at strengthening democratic institutions, 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 areas were considered some of the least secure on polling day. Anecdotal accounts of nearly empty polling stations there suggested low voter turnout, but few international observers went to these areas because of security risks.
Though there are no official voter turnout figures, government officials and independent observers have generally said voters showed up in low numbers because of Taliban threats ahead of election day. Dozens of people were killed in rocket attacks, bombings and polling station raids.
The NDI monitoring group said it had "deep concern" over the high levels of fraud complaints. "It will be impossible to determine the will of the Afghan people" unless fraud complaints are thoroughly investigated, it said in a statement.
The continued election uncertainty comes amid a new report from a policy think tank that shows the Taliban has a significant presence in almost every corner of Afghanistan.
A security map by the International Council on Security and Development showed a deepening security crisis with substantial Taliban activity in at least 97 percent of the country. The ICOS data, obtained by Reuters before its release on Thursday, painted a darker picture than an Afghan government map that showed last month almost half of Afghanistan at either a high risk of attack or under "enemy control."
The election, initially hailed a success after the Taliban failed to disrupt it, has also turned into a major headache for Washington and a test of President Barack Obama's new regional strategy to defeat the militants and stabilize Afghanistan.
The election disputes also coincides with the most violent period since the Taliban were toppled by U.S.-backed Afghan forces in 2001, with record military and civilian deaths testing the resolve of U.S. and European leaders.
---- Compiled from wire reports and other media sources