Initial results based on 10% of the vote from 26 out of 34 provinces showed Abdullah in the lead with 41.9%, the Independent Election Commission said, while Western-leaning Ashraf Ghani came second with 37.6%. A third candidate, running with the backing of President Hamid Karzai's brothers, had 9.8%.
"I want to make clear that the results could change in future, as we announce the results with additional percentages of the vote and this is not the final result," said the chairman of the election commission, Ahmad Yousuf Nuristani.
Afghanistan's allies praised the April 5 vote as a success because of the high turnout, estimated at 60% of 12 million eligible votes, and the failure of Taliban militants to stage high-profile attacks on the day.
But evidence of widespread fraud could undermine the legitimacy of an election meant to usher in Afghanistan's first democratic transfer of power, as incumbent Hamid Karzai prepares to step down after more than 12 years in power, and as Western forces prepare to leave.
The election complaints body hinted it might need more time to investigate all of the complaints. Final results are due on May 14.