Afghanistan's Independent Election Commission said initial results based on 10 percent of
the vote from 26 out of 34 provinces showed former opposition leader Abdullah Abdullah in the lead with 41.9 percent.
Former opposition leader Abdullah Abdullah is in the lead in Afghanistan's elections.
The country's Independent Election Commission said initial results based on 10 per cent of votes from 26 out of 34 provinces showed Mr Abdullah in the lead with 41.9 percent of the vote.
In second place was Western-leaning academic Ashraf Ghani with 37.6 percent of the vote, the IEC said, while a third candidate, running with the backing of two of President Hamid Karzai's brothers, trailed far behind with 9.8 percent.
Afghan authorities have received more than 3,000 reports of violations from last weekend's presidential election, exceeding the tally following a 2009 vote that was marred by widespread fraud.
The three frontrunners have all complained of fraud in the April 5 vote mean to usher in Afghanistan's first democratic transfer of power, as Hamid Karzai prepares to step down after more than 12 years as head of state.
"As soon as we get them, it is clear the final number is going to increase," said Nader Mohseni, spokesman for the Independent Election Complaints Commission. He said around half of the 3,103 complaints registered so far would be probed because the rest had lacked the required supporting evidence.
NATO's Secretary General congratulated the Afghan people after millions turned out to vote in an historic election.
Anders Fogh Rasmussen said in a statement: "The Afghan people can be proud of their security forces, who have done an outstanding job in securing the elections [...] This has truly been an election led by Afghans, secured by Afghans, for the future of Afghans."
Foreign Secretary William Hague has welcomed the high turnout for presidential elections in Afghanistan, taking place just months before the withdrawal of international troops.
Mr Hague said: "This is an historic moment for Afghanistan and its people. Across the country, millions of Afghans have been voting for a new president.
"It is a great achievement for the Afghan people that so many voters, men and women, young and old, have turned out in such large numbers, despite threats of violence, to have their say in the country's future," Mr Hague added.
"Now that all the votes have been cast, I hope all parties will show patience and respect while the electoral authorities go to work to count and check the ballots, and declare the results."
Afghan President Hamid Karzai has said the election was a "success" amid relief that attacks by Taliban fighters were fewer than feared, for a vote that will bring the first-ever democratic transfer of power in a country plagued by conflict for decades.
In a statement after voting closed, President Karzai said: "The Afghan nation today have put in practice their big Jubilee of the nation's participation in voting.
"Despite the cold and rainy weather and possible terrorist attack, our sisters and brothers nationwide took in this election and their participation is a step forward and it is a success for Afghanistan."
Women voters have been lining up at polling stations across Afghanistan, defying a threat of violence by the Taliban to cast ballots in what promises to be the nation's first democratic transfer of power.
The Taliban warned civilians ahead of the election they would be targeted if they try to vote, and dozens died in a spate of attacks in the preceding weeks.
Long queues continue to form outside polling stations around Kabul, as people defied Taliban threats of violence to cast ballots in what promises to be the country's first democratic transfer of power.
As international combat forces prepare to withdraw by the end of this year, the country is so unstable that the very fact the crucial elections are being held is touted as one of the few successes in Mr Karzai's tenure.
Nearly 200,000 Afghan security forces are out protect polling stations and voters from threatened Taliban attacks.