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Election officials in Afghanistan collected ballots on Sunday from a historic presidential vote which started enthusiastically but ended in turmoil after most of the candidates announced a boycott.

No turnout figures have been released from Saturday's voting, but the desire of people to elect their leader for the first time in their impoverished and rugged Islamic country's history was clear.

From the southern plains to the Hindu Kush mountains and northern steppes, millions turned out to vote despite threats by Taliban fighters to sabotage the election. Attacks on the vote did not materialise but up to 40 people were killed in clashes, including 24 in a U.S. bombing raid.

Afghan refugees living in Pakistan queue to vote in Afghanistan’s presidential elections in the western border city of Chaman October 9. A woman of 19 who fled Afghanistan’s long civil war made history on Saturday by casting the first vote in her country’s first direct presidential election, before rivals of the incumbent threw the poll in to confusion by declaring a boycott. (REUTERS)

But midway through the day all 15 rivals of U.S.-backed President Hamid Karzai said they were boycotting the poll because a system to prevent voting fraud had failed.

Karzai, who is favourite to win, said his rivals should respect the will of the people.

"I would advise my fellow countrymen, the 15 other candidates, that we must all respect the fact that millions of Afghans came out on foot, in rain and snow and dust and waited for hours to vote," Karzai said.

"That's a tremendous thing for us in this country for the first time, and we must all respect that and wait for the commission to count the votes and make a judgment on the irregularities and then we proceed further from that point."

At issue was indelible ink put on the finger of everyone who voted to ensure they could not vote again. But some election workers used the wrong pen to mark voters, and the ordinary marker ink was quickly washed off.

And with questions over the late and rapid registration of 10.5 million voter cards in a population of about 28 million, there were allegations of voter fraud.

"We strongly condemn today's election which we consider was an illegal election," candidate Abdul Satar Serat said. "It was against Afghanistan's national benefits, it was against democracy in Afghanistan and it was against international law.

The Joint Election Management Body of U.N. and Afghan experts said the allegations of irregularities were serious and would be investigated.

But it said counting, likely to begin on Monday, would go ahead. Some officials said it could take up to three weeks to settle questions on irregularities.

The election comes three years after the United States began bombing Afghanistan as a prelude to ousting the hardline Islamic Taliban for failing to hand over Osama bin Laden, architect of the Sept. 11 attacks. About 18,000 U.S.-led troops are in Afghanistan hunting for bin Laden and other militant leaders.

U.S. President George W. Bush, facing his own election next month, has claimed the Afghan vote as a foreign policy success and is hoping it can be mirrored in Iraq, where polls are set for January.

Meanwhile up to 40 people were killed in fresh militant violence in Afghanistan's restive south, but the threat of Taliban attacks did not deter men and women from voting in Saturday's historic election.

The single largest clash reported on polling day was in Uruzgan province, where governor Jan Mohammad Khan told Reuters that 24 suspected Taliban guerrillas were killed, as well as one civilian, in an air strike by U.S.-led forces.

But residents in the area countered that 14 civilians, 13 of them women or children, died in the bombing, according to accounts to Reuters and the Pakistan-based Afghan Islamic Press news agency.

Khan said the gunmen attacked U.S. and Afghan troops in Char Cheno district at about 1.30 a.m. (2100 GMT on Friday), and sustained heavy losses when close air support was called in. Colonel Richard Pedersen, commander of U.S.-led forces in southern Afghanistan, said he was aware of the clash, but declined further comment.