Kai Eide called a media conference to deny allegations made by his sacked former deputy, Peter Galbraith, that he had concealed evidence of fraud in the presidential elections.
He said the UN supported investigations into the allegations which were under way and expected to be completed - and a final result announced - within days.
The elections, held on August 20, have been overshadowed by allegations of widespread fraud, mostly aimed at President Hamid Karzai. Mr Karzai leads preliminary results with about 55 per cent of the vote, against his nearest rival Abdullah Abdullah, who is on 28 per cent.
"It is true that in a number of polling stations in the south and the southeast there was significant fraud," Mr Eide said.
"The extent of that fraud is now being determined," he said, referring to investigations being conducted by the Electoral Complaints Commission and an audit of suspicious ballot boxes by the Independent Election Commission last week.
"It has been claimed that there was 30 per cent fraud. There is no way to know at this stage what the level of fraud is," he said. "No one knows. I can only say there was widespread fraud."
Mr Eide called the media conference to answer accusations by Mr Galbraith, who was dismissed last month after a row with his boss over how to deal with the fraud allegations, that he tried to conceal information about the extent of the fraud.
He was flanked by the ambassadors to Kabul from the US, Britain and France, with the German ambassador, the EU special representative to Afghanistan, and a NATO representative also in attendance. None of the ambassadors made any comment, and reporters were not permitted to ask them questions.
Visibly angry, Mr Eide said: "Some of these allegations were based on private conversation whilst he was a guest in my house.
"My view is that private conversations around a dinner table in my house remain just that - private."
The publicity surrounding Mr Galbraith's dismissal, and the accusations he made against Mr Eide "have not only been personal attacks against me and my personal integrity but have affected the whole election process", he said.
Mr Galbraith was sacked on September 30 by UN chief Ban Ki-moon and immediately went on the offensive, saying the decision sent a "terrible signal" about the commitment of the UN to a fraud-free election.
Differences between the two men began before the poll when Mr Galbraith wanted to eliminate "ghost" polling centres that posed a risk of fraud as they were too insecure to open on election day.
When fraud evidence became "very extensive", he said - citing high vote numbers from regions where turnout was known to be low - Mr Eide would not allow the information to be disseminated, even to ambassadors based in Kabul.
He also said that 30 per cent of Mr Karzai's votes were fraudulent, echoing findings by EU election monitors that about 1.5 million votes in total - and 1.1 million for Mr Karzai - were suspicious.
Mr Eide denied any suggestion that he had interfered with the process to conceal the level of fraud, saying the UN mandate "is to support the process, not influence the outcome".
Source: The Australian