Ballot boxes had been stuffed and the whole system was working to benefit his rival Ashraf Ghani, Dr. Abdullah Abdullah said.
He said he had lost trust in election officials, adding: “We have asked our monitors to leave their offices.”
A run-off vote to choose who replaces Hamid Karzai was held on Saturday. Final results are due in July.
Abdullah Abdullah won most votes in the first round in April, but did not secure an outright majority.
There was no immediate comment from Ashraf Ghani, a former World Bank economist.
Hamid Karzai, who has served two terms as Afghanistan’s first and only president since the Taliban were ousted in 2001, is obliged by law to stand down after the latest election, which would be the country’s first peaceful transfer of power.
He is expected to hand over to his successor in August.
Dr. Abdullah Abdullah said that a number of his observers had been beaten up, detained and only released on Tuesday.
He accused President Hamid Karzai of not being neutral and said important concerns he had raised over the election had been ignored.
Abdullah Abdullah also complained that there had been no clarification over what he had called inflated turnout figures – and no explanation for the sacking of several thousand election workers after the first round.
He added that he had also demanded that a senior member of the Independent Election Commission should be suspended, but this had not happened.
“The counting process should stop immediately and if that continues, it will have no legitimacy,” Dr. Abdullah Abdullah told reporters.
Ballot boxes have yet to reach Kabul for votes to be counted but the former foreign minister said preliminary evidence gathered by his team showed widespread fraud.
According to initial reports received by his staff, Ashraf Ghani is leading by nearly a million votes after Saturday’s run-off, Reuters news agency reported.
Dr. Abdullah Abdullah pulled out of Afghanistan’s 2009 presidential election which was also marred by claims of mass fraud.
UN and US officials have been urging both contenders in this year’s race to give officials time to count votes and look into possible malpractice.
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