NEW YORK - The Bush administration repeatedly sought to block investigations into alleged killings of up to 2,000 Taliban prisoners by a US-backed Afghan warlord in 2001, The New York Times reported Saturday. Top US officials discouraged separate probes by the Federal Bureau of Investigation (FBI) and the State Department into the episode because it was conducted by the forces of General Abdul Rashid Dostam, a warlord then on the Central Intelligence Agencys payroll, the Times newspaper said. A fully-fledged inquiry by the Defence Department was never completed, it said.Dostams militia had worked closely with US Special Forces during the US-led invasion and was part of the Northern Alliance, which, with US backing, helped topple the Taliban. Washington was later concerned an investigation could hurt Afghan President Hamid Karzai, who had the support of George Bushs administration, as Dostam has served as a defence official in the fledgling government. At the White House, nobody said 'no to an investigation, but nobody ever said 'yes, either, former US war crimes ambassador Pierre-Richard Prosper told the newspaper. The first reaction of everybody there was 'Oh, this is a sensitive issue. This is a touchy issue politically. The new US administration has maintained frostier relations with Karzai, whose government is seen as corrupt and unpopular, although Obama has dispatched 21,000 fresh troops to fight a mounting Taliban-led insurgency ahead of August elections. Secretary of State Hillary Clinton and Richard Holbrooke, the special US envoy to Afghanistan and Pakistan, have told Karzai they objected to the recent reinstatement of Dostam as military chief of staff, the Times said, citing a senior State Department official. We believe that anyone suspected of war crimes should be thoroughly investigated, the official added, hinting the Obama administration is open to an inquiry. Dostam, whose alleged killings may have amounted to the biggest war crime in Afghanistan since the 2001 invasion, was reinstated to his post last month after being suspended last year for allegedly threatening a political opponent at gunpoint. But he remains in exile in Turkey. The killings took place in late November 2001, shortly after the invasion that ousted Kabuls Taliban government. Taliban prisoners captured by Dostams forces after a major battle in northeastern Kunduz province were allegedly packed into shipping containers and left to suffocate, or were shot through the container walls, before being buried in mass graves. Estimates on the number of people killed have ranged from several hundred to several thousand. Survivors and witnesses told The New York Times and Newsweek in 2002 that over a three-day period, Taliban prisoners were stuffed into closed metal shipping containers and given no food or water; many suffocated while being trucked to the prison. Other prisoners were killed when guards shot into the containers. The bodies were said to have been buried in a mass grave in Dasht-i-Leili, a stretch of desert just outside Shibarghan. A recently declassified 2002 State Department intelligence report states that one source, whose identity is redacted, concluded that about 1,500 Taliban prisoners died. Estimates from other witnesses or human rights groups range from several hundred to several thousand. The report also says that several Afghan witnesses were later tortured or killed. The Pentagon, however, showed little interest in the matter. In 2002, Physicians for Human Rights asked Defence Department officials to open an investigation and provide security for its forensics team to conduct a more thorough examination of the gravesite. We met with blanket denials from the Pentagon, recalls Jennifer Leaning, a board member with the group. They said nothing happened. Pentagon spokesmen have said that the United States Central Command conducted an informal inquiry, asking Special Forces personnel members who worked with General Dostum if they knew of a mass killing by his forces. When they said they did not, the inquiry went no further.