After a mass killing of hundreds, perhaps thousands, of Taliban prisoners of war by the forces of an American-backed warlord during the 2001 invasion of Afghanistan, Bush administration officials repeatedly discouraged efforts to investigate the episode, according to government officials and human rights organizations.

American officials had been reluctant to pursue an investigation -- sought by officials from the F.B.I., the State Department, the Red Cross and human rights groups -- because the warlord, Gen. Abdul Rashid Dostum, was on the payroll of the C.I.A. and his militia worked closely with United States Special Forces in 2001, several officials said...

While the deaths have been previously reported, the back story of the frustrated efforts to investigate them has not been fully told. The killings occurred in late November 2001, just days after the American-led invasion forced the ouster of the Taliban government in Kabul. Thousands of Taliban fighters surrendered to General Dostum's forces...

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-Laili, a stretch of desert just outside Shibarghan...

Separately, 10 or so prisoners brought from Afghanistan reported that they had been "stacked like cordwood" in shipping containers and had to lick the perspiration off one another to survive...

The Pentagon, however, showed little interest in the matter...

Another former defense official, who would speak only on condition of anonymity, recalled that the prisoner deaths came up in a conversation with Paul D. Wolfowitz, the deputy secretary of defense at the time, in early 2003.

"Somebody mentioned Dostum and the story about the containers and the possibility that this was a war crime," the official said. "And Wolfowitz said we are not going to be going after him for that."

...

As evidence mounted about the deaths, Secretary of State Colin L. Powell assigned Mr. Prosper, the United States ambassador at large for war crimes, to look into them in 2002. He met with General Dostum, who denied the allegations, Mr. Prosper recalled. Meanwhile, Karzai government officials told him that they opposed any investigation...

Mr. Prosper said that because of the resistance from American and Afghan officials, his office dropped its inquiry.