America's top diplomat at the United Nations mission in Afghanistan has been ordered out of the country after a row with his boss over how to respond to last month's fraud-riddled presidential elections, it has been alleged.

The alleged quarrel is threatening to spark a mutiny within the UN mission. At least a dozen senior staff are backing the American, Peter Galbraith, in the dispute with his Norwegian superior, Kai Eide.

Mr Galbraith, a close friend of the US special envoy Richard Holbrooke, left for Boston on Sunday after a heated meeting with Afghan election officials. His “pointed” questions to the Independent Election Commission (IEC) were evidence of a much tougher line towards the Afghan authorities than the “softly-softly” approach of Mr Eide, who heads the UN mission to Kabul.

“The relationship between Kai and Peter has completely broken down,” said a diplomat in Kabul. “Peter has left the country. The official line is that he's on a three-week mission to New York. But Kai just turned round to Peter and said, ‘I want you out'.”

The apparent row illustrates the deepening divisions within the international community on whether to allow President Karzai to claim re-election in the flawed presidential poll.

Mr Galbraith wants the IEC to annul results from 1,000 of the total of about 6,500 polling stations and to recount results from another 5,000, diplomatic sources said. Mr Eide, a former UN envoy in Bosnia, seeks only a face-saving recount of some 1,000 polling places, the sources said.

Mr Galbraith's wholesale recount would virtually ensure a second round in the election, denying Mr Karzai his claimed first-round victory. Harsh winter weather means that the second round could not be held before May, leaving Afghanistan in political limbo.

Mr Eide's solution would probably enable Mr Karzai to claim victory, although with a reduced margin.

Mr Eide and Mr Galbraith insist that they are old friends from serving in the Balkans. Indeed, Mr Eide introduced Mr Galbraith to the Norwegian anthropologist who became his wife. But Mr Eide is said to have lobbied behind the scenes to block Mr Galbraith's appointment as his deputy in March and their relationship appears to have deteriorated.

The row worsened when Mr Eide left Afghanistan to celebrate his wedding anniversary in Norway after the election and refused to cut short his break despite the fraud allegations..

Mr Eide was out of the country when the election-rigging issue reached a head last Tuesday.

The IEC were preparing to announce the last 15 per cent of ballots, coming from the most controversial areas of the south and Badghis province in the north. All are expected to return big majorities for Mr Karzai. Mr Galbraith then stepped in and forced the more robust line from the IEC, forcing them to agree not to announce the controversial last results.

At a meeting with IEC officials on Sunday, Mr Galbraith “laid into the commissioners, in front of the donors and observers” and demanded to know why they had not started printing ballot papers as part of a run-off contingency plan.

Mr Eide, now back in Kabul, has urged his staff not to speak out against the fraud because he fears that it will destabilise efforts to build a democracy. He is also afraid that fraud investigations will be seen as foreign interference, because three of the five people in charge of the Election Complaints Commission are UN appointees.

“The one thing the UN should be doing, which it's not doing, is speaking up on election fraud,” said a mission insider. “A lot of people in the UN feel that unless there's space for someone to behave as Peter has behaved, then what are we doing here?”

UN officials suggested that Mr Galbraith was more in tune with America's tough stance on fraud, while Mr Eide's less vocal position echoes that of the European missions in Kabul.

British embassy officials insisted that they were in line with the American position. “As the Foreign Secretary has made clear, we will not be party to any whitewash when it comes to the elections,” a spokesman said.

Mr Eide and Mr Galbraith met on Saturday night, shortly after the latest set of official results confirmed Mr Karzai's lead with 54.3 per cent of the vote. Mr Eide is said to have asked Mr Galbraith to “leave the country for a while”, according to a European official.

When news of Mr Galbraith's sudden departure spread around the UN mission, a dozen senior diplomats went to his office to show him their support, before his flight. “He has provided the principled leadership UN staff expect,” said one of the officials.

Farhan Haq, a UN spokesman in New York, said that Mr Galbraith was in Boston “on mission” and would travel to London next week before going to New York to brief the UN Security Council on September 29 with Mr Eide.