3 percent of the vote, while Abdullah, a former foreign minister, received 28.1 percent.
The second election in Afghanistan's history was marred by massive allegations of fraud.
ECC chief Grant Kippen said Monday that the commission ordered election officials to audit and recount ballots from polling sites where there was a turnout of 100 percent, or where one candidate received more than 95 percent of valid votes.
He said the huge volume of the fraud complaints that need to be investigated would delay by several weeks the final results, which were originally scheduled to be announced Sep 17.
But Barekzai said the recount would not affect the announcement of preliminary results, now expected Wednesday afternoon.