About 680 ballot boxes, almost 3% of the total, have been taken out of the counting process because of suspicions they were stuffed, said Richard Atwood, chief of operations for the joint UN-Afghan election commission.
But he said: "The fraud that has occurred does not affect the integrity of the election." He ruled out a re-count.
"The fraud is not systematic or widespread across the country," Atwood said in Kabul. Election organisers have done all they can to ensure the fraud is caught, he added.
He said that approximately 50 staff had been dismissed because of fraud, but did not elaborate.
Atwood said investigations into the fraud had slowed the counting of the ballots.
Almost a month after the 18 September vote, provisional results have been published in only 20 of the 34 provinces.
Accusations of irregularities in the count have sparked demonstrations in several cities, including the capital, Kabul.
"These elections no longer have any meaning. So many bribes have been given. Some candidates have bought their way to power," said Bashir Bezhen, an official with the state Ariana airlines who stood as an independent candidate in Kabul but lost.
Afghans who voted say the poll
no longer has meaning
"The counters were shameless in their work. They were like businessmen, making deals with whoever had money. There should be a re-count."
Many of those who have been declared winners in the provisional results are suspected regional commanders, including Abdul Rasul Sayyaf, a powerful militia leader who New York-based Human Rights Watch has accused of war crimes.
Electoral law bars anyone with links to armed groups from competing; but with nearly 2800 candidates, activists say many of the regional commanders involved in the bloodshed of the past quarter-century have slipped through a UN-backed review they call woefully inadequate.
At least two former members of the Taliban have been elected, according to the results.
One is Abdul Salaam Rocketi, a front-line general who spent eight months in US detention and now actively encourages other Taliban members to reconcile with the government.
Another is Mawlawi Mohammed Islam Mohammadi, the ex-Taliban governor in Bamiyan province where members of the former government in 2001 blew up two giant 1500-year-old Buddha statues because they said they were an affront to Islam.
Suspected smugglers detained
Meanwhile, Afghan police have arrested two British nationals, an American and an Indian, all with fake badges for the Nato-led peacekeeping force, on weapons smuggling charges, officials said on Sunday.
The men were arrested on Wednesday with two Afghans who were allegedly their accomplices, Interior Ministry spokesman Yousuf Stanizai told AFP.
"The foreign citizens are civilians and are working for a construction company. They were arrested with five AK-47 machine guns and two pistols," he said.
"They were carrying fake ISAF badges and they were smuggling out Russian weapons and drugs"
Interior Ministry spokesman
The men were carrying fake badges for the International Security Assistance Force (ISAF) of peacekeepers deployed in the capital and northern and western Afghanistan, an intelligence official said.
"They were carrying fake ISAF badges and they were smuggling out Russian weapons and drugs," he said.
British embassy spokesman Keith Scott said late on Saturday that two British nationals had been arrested and were receiving consular assistance. He could not give details of the charges against them or details of the arrest.