Voting cards are being sold openly and candidates have been offering thousands of dollars in bribes for votes.
The findings came as campaigning closed before Thursday's election, in which incumbent President Hamid Karzai faces 41 challengers.
A senior Afghan Independent Election Commission official denied to the BBC that voting cards were being sold.
The allegations came as militants launched a flurry of deadly attacks across Afghanistan on Tuesday, in the wake of their threats to disrupt the election.
Afzali is not an illiterate farmer, indoctrinated by the Taliban about “puppet presidents” and “infidel elections”, but a student at Herat University. And he is by no means alone in his views.
Multiple voting cards
An Afghan working for the BBC went undercover in Kabul to investigate reports that voting cards were being sold and was offered 1,000 cards, each costing around £6 ($10).
Other vendors made similar offers.
It is impossible to know how many voting cards have been sold in such a manner, says the BBC's Ian Pannell in Kabul, but there have been a number of arrests.
Multiple voting cards are reported to have been issued to some individuals, while government workers have actively and illegally campaigned for candidates, says our correspondent.
An influential tribal leader in the north of the country said he had been offered thousands of dollars by campaign teams in exchange for delivering large blocks of votes.
Separately, an independent monitoring group said it had shown evidence of corruption to election officials, but they had not acted on the information.
However, a senior Afghan Independent Election Commission official, Daud-Ali Najafi, dismissed claims of voting fraud.
He said: "We totally reject the allegations that cards are being bought. Even if one is bought it can't be used. The person who owns the card must vote him or herself."
Western officials have conceded that the election will be flawed but say a flawed election is still better than no vote at all.
Mr Karzai, who is seen as the frontrunner, and his two main rivals held their last rallies of the campaign on Monday.
The current president was forced to defend his links with notorious warlord, Gen Abdul Rashid Dostum, during a TV debate.
The election is taking place amid an upsurge in violence - with a survey by the BBC's Afghan service suggesting the government has little or no control of 30% of the country.
A spokesman for Mr Karzai said the government did not agree with the findings, saying there were security problems in just a few districts.