A survey by the BBC's Afghan service suggests the government has limited or no control in 30% of the country.
The survey is based on assessments by reporters in the field who found that in 4% of Afghanistan's districts, the government provides no security or services.
The majority of them are in the south, where most Taliban attacks have taken place.
A spokesman for President Karzai said the government did not agree with the findings and there were security problems in just a few districts.
The BBC's Ian Pannell in Afghanistan says that there is evidence of corruption, but above all it is the ongoing war with the Taliban - within at least a third of the country - that makes this election far from normal.
But having invested so heavily in terms of time, money and even lives, Western officials are likely to declare the vote a success - whatever the flaws and challenges, he adds.
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