On top of that, a violent Taliban campaign aimed at keeping people away from polling stations is believed to have kept turnout as low as 30-35 per cent.
With almost all ballots counted, preliminary results released earlier this week gave Hamid Karzai, the incumbent president, 54 per cent of votes. That would be enough to avoid a runoff with his closest rival, Abdullah Abdullah, a former foreign minister.
The ECC did not say how many votes it had invalidated in total so far. Based on preliminary results, more than 400,000 ballots for Karzai would have to be annulled to require a second round.
Most of the discarded polling stations were in areas where pro-Karzai voting was particularly visible.
Fifty-one of the 83 polling stations with alleged fraud were found in southern Kandahar, which is Karzai's home province but also a Taliban stronghold.
In Paktika, Karzai got 91.9 per cent against Abdullah's 3.8 per cent, according to preliminary results.
Abdullah was quoted as saying he wanted a fair result to be found through peaceful channels.
"I'm not talking about just my own supporters, but those who cast their vote for Mr Karzai," he told BBC radio.
"Their vote is now part of the fraud. And on top of that, a fraudulent outcome: illegitimate rule for another five years.
"I think this in itself is a recipe for instability in this country."
Wahid Omar, Karzai's campaign spokesman, told BBC radio that allegations had made the work of the investigators difficult.
"We actually believe that most of the remarks that have been made should not be taken as the reality," he said.
"These are all rumours and I think we should not base our statements on rumours that we have no way to verify."
The ECC has ordered a recount from polling stations where one candidate received more than 95 per cent of the vote or more votes were cast than the expected maximum.
Western powers originally praised the election, but confidence in the handling of the vote has eroded as allegations of fraud have continued to mount.
David Owen, a member of the UK upper house of parliament, told Al Jazeera that "the level of corruption... straight out electoral vote rigging, is worrying".
"I think Hillary Clinton, the US secretary of state, was wise to persuade Karzai not to claim victory and let the process work its way through."
Still, he said that "Afghanistan has never really been what we would think of as an electoral democracy - we shouldn't be too upset if these elections are not too successful".
"At the end, we'll have the choice to accept a very unsatisfactory democratic election or to try and overturn it... we have to reach some kind of compromise to find an end to this election.
"President Karzai has got to be realistic. One way is to try and reach a coalition and let his other presidential candidate come into that coalition government but that is not easy to do," he said.