The Afghan Government has called on Nato troops to guard an alleged war crimes site that has been plundered and as many as 2,000 bodies apparently removed.

The mass grave at Dasht-e-Leili in northern Afghanistan is thought to contain the remains of between 1,000 and 2,000 Taleban prisoners massacred by fighters loyal to the Uzbek warlord General Abdul Rashid Dostum in November 2001. The killings occurred in the remote Leili desert as General Dostum’s forces fought alongside US special forces.

Prisoners were packed into sealed shipping containers and left to suffocate. Others are alleged to have died when fighters riddled other containers full of prisoners with bullets before burning and burying the bodies.

A State Department intelligence assessment from November 23, 2002, released recently under freedom of information laws, assessed that up to 2,000 Taleban prisoners died in the incident, despite initial claims from the US Government that the number was in the dozens. The mass grave site is a forbidding and desolate spot in an area notorious for bandits and thieves.

Human rights organisations confirm that five large pits have appeared recently at the site, with two measuring about 15m (50ft) by 30m, and that earth movers have been operating, digging to a depth of 3m.

“We have evidence that significant removal of evidence has taken place,” said Nathaniel Raymond, a senior investigator at Physicians for Human Rights, a US-based organisation specialising in mass grave investigations that has been hired by the United Nations to monitor several war crimes sites in Afghanistan.

“We don’t know how much is left. We don’t know how much has been removed. The Afghan Government, the international community and the United States in particular has responsibility to stop actors such as Abdul Rashid Dostum from trampling on international law.”

Farid Mutakhail, head of the Afghan Independent Human Rights Commission in the north, said that the digging might have been going on for four or five months. “We found that most of the bones that were excavated from the grave were thrown into the Pul-e-Surkh river,” he said.

Humayun Hamidzada, a spokesman for the Afghan Government, told The Times: “We are aware of the importance of the site and we are in the process of requesting Nato forces to protect the site.”

Nato officials said that they had not received a formal request. There are 84 known mass grave sites in Afghanistan but none has been excavated and few are monitored by the authorities.

Claims that a massacre had taken place at Dasht-e-Leili emerged in 2002. An initial investigation produced 15 bodies from one trench. Post-mortem examinations on three found that the cause of death was suffocation, which was judged to be homicide.

General Dostum, the alleged perpetrator of the massacre, was chief of staff to the Afghan National Army until this year. He retains strong support among the Uzbek population in the north and won 10 per cent of the vote in the 2004 presidential elections.

At the height of his power in the 1990s, Dostum ran his own mini-state in northern Afghanistan, printing his own currency, setting up an airline and travelling in an armoured Cadillac. Faced with the advance of the Taleban he is reported to have vowed never to submit to a government that banned whisky and music.

In February he was suspended from his post and a warrant was issued for his arrest when, backed by 50 gunmen, he broke into the home of a political rival, Akbar Bai, and assaulted him and his family. General Dostum retreated to his palace in Kabul, which also houses his television station.

This month the Turkish press reported that he had gone into exile in Turkey. That was denied last night by Azizullah Kargar, the deputy leader of the general’s Junbish-e-Millie party. “General Dostum was officially invited by the Turkish Foreign Ministry. He went to meet some Turkish officials and to see his family. He will return very soon to Afghanistan,” he said.

A spokesman for the Presidential Palace in Kabul declined to comment.

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