Human rights researchers who originally uncovered the case say they’ve seen no evidence of an active investigation.

The deaths happened as Taliban forces were collapsing in the wake of the American invasion of Afghanistan. Thousands of Taliban prisoners had surrendered to the forces of a U.S.-supported warlord named Abdul Rashid Dostum. The prisoners, say survivors and other witnesses, were stuffed into shipping containers without food or water. Many died of suffocation. Others were allegedly killed when Dostum’s men shot at the containers.

A few months later, a mass grave was found nearby in Dasht-i-Leili, a desert region of northern Afghanistan.

The New York Times reported in 2009 that the Bush administration, sensitive to criticism of a U.S. ally, had discouraged investigations into the incident. In response, Obama told CNN that “if it appears that our conduct in some way supported violations of the laws of war, I think that we have to know about that.”

A White House spokeswoman told ProPublica that there has indeed been some kind of review – and that it’s still ongoing: “At the direction of the President, his national security team is continuing its work looking into the Dasht-i-Leili massacre.” She declined to provide more details.

“This seems quite half-hearted and cynical,” said Susannah Sirkin, director of international policy at Physicians for Human Rights, the group that discovered the grave site in 2002 and since then has pushed for an investigation.

The group sent a letter to the president in December 2011, the tenth anniversary of the incident. In a follow-up meeting some months later, senior State Department officials told Physicians for Human Rights that there was nothing new to share.

“This has been a hot potato that no one wanted to deal with, and now it’s gone cold,” said Norah Niland, former director of human rights for the United Nations in Afghanistan.

Human rights advocates have long said the responsibility for a comprehensive investigation lies with the U.S., because American forces were allied with Dostum and his men at the time. Surviving prisoners have also claimed that Americans were present when the containers were loaded, though that’s never been corroborated.

A Pentagon spokesman told ProPublica that the Department of Defense “found no evidence of U.S. service member participation, knowledge, or presence. A broader review of the facts is beyond D.O.D.’s purview.” That initial review has never been made public.

At this point, say advocates, an investigation should address not just the question of U.S. involvement, but also what the U.S. did in the years that followed to foster accountability.

“I’m not saying Dostum ordered these people killed, and I’m not saying U.S. troops participated,” said Stefan Schmitt, a forensic specialist with Physicians for Human Rights. “All I’m saying is there are hundreds if not thousands of people that went missing. In a country that’s looking to have peace, to be under the rule of law, you need to answer these questions.”

Initially excited by Obama’s statement, researchers with Physicians for Human Rights peppered the administration with their findings. But the response was “murky at best,” said Sirkin.

“We were never very clear on who within the administration was delegated the task,” she said. Current and former administration officials interviewed by ProPublica couldn’t say which agency or department had the job.

Sirkin and others eventually resigned themselves to the fact that Obama, in his televised remarks, had not specifically called for a full investigation. With the U.S. now withdrawing from Afghanistan, many observers say it’s no surprise that investigating Dasht-i-Leili is no longer a priority.

Dostum still holds considerable sway in Northern Afghanistan, though he has fallen in and out of favor with the U.S. and with Afghan president Hamid Karzai. The Times recently reported Dostum is one of several former warlords to whom Karzai passes on thousands of dollars in cash he receives from the CIA each month. (We were unable to reach Dostum himself for this story.)

The Obama administration has been cool toward him in recent years, saying ahead of Afghanistan’s elections in 2009 that the U.S. “maintains concerns about any leadership role for Mr. Dostum in today’s Afghanistan.”

Back in 2001, Dostum was far more important to the U.S. He was a U.S. proxy, fighting the Taliban as part of the Northern Alliance. American Special Forces famously rode on horseback alongside Dostum’s men, advising and calling in airstrikes. The alliance took the city of Mazar-i-Sharif from the Taliban in one of the first major victories of the invasion in early November 2001.

The shipping container deaths occurred a few weeks later, when Taliban fighters who had surrendered to the Northern Alliance at the city of Kunduz were en route to a prison about 200 miles away.

That winter, Physicians for Human Rights discovered a mass grave at Dasht-i-Leili. A preliminary investigation exhumed several bodies that appeared to have died from suffocation. Stories began to circulate in the region and Newsweek and others published detailed accounts from surviving prisoners, truck drivers, and other witnesses.

The Times also reported that an FBI agent interviewing new Afghan arrivals to Guantanamo Bay prison in early 2002 heard consistent accounts of prisoners “stacked like cordwood,” and death by suffocation and shooting. When the agent pressed for an investigation, he was reportedly told it was not his responsibility.

Dostum has said that he would welcome an investigation. He said that some 200 prisoners had indeed died in transit, but that the deaths were unintentional, the result of battlefield wounds.

Other estimates put the toll much higher.

A widely cited State Department memo from fall 2002 said that “the actual number may approach 2,000.”

Around the same time, then-Secretary of State Colin Powell tasked his Ambassador for War Crimes, Pierre-Richard Prosper, with looking into Dasht-i-Leili. Prosper told ProPublica that due to the U.S. alliance with Dostum, Washington felt the U.S. should not take the lead in an investigation.

“We were in the middle of fighting, and we thought we should keep the lines clear, let someone else, the U.N. or Afghans, handle this,” said Prosper.

But the newly installed Afghan government had neither the will nor the resources for a thorough investigation, and U.N. officials said they could not guarantee security. Witnesses and others involved in Dasht-i-Leili had already been killed and harassed, according to State Department memos.

A declassified Defense Department memo from February 2003 indicates the U.S. was not providing security for an investigation. The memo’s author, Marshall Billingslea, told the Times in 2009, “I did get the sense that there was little appetite for this matter within parts of D.O.D.” (Billingslea did not respond to our requests for comment.)

As the years went by, no one from the U.S., the U.N., or Afghanistan guarded the grave site. In 2008, reporters and researchers found empty pits where they had once found human remains. Satellite photos obtained later showed what appeared to be earth-moving equipment in the desert in 2006. Locals told McClatchy that Dostum’s men had dug up the graves.

After Obama pledged in 2009 to look into the case, a parallel inquiry was begun the next year in the Senate Foreign Relations Committee, chaired by current Secretary of State John Kerry.

The fate of that investigation is also unclear. The lead investigator, John Kiriakou, was a former CIA officer who was caught up in a criminal leak prosecution and is now in prison. Other Senate staffers could not provide details on Kiriakou’s efforts. Physicians for Human Rights says contact from the committee fizzled out within a year.

New attention to Dasht-i-Leili had also been sparked within the U.N.’s mission in Afghanistan and the organization’s High Commission on Human Rights, former U.N. officials said.

However, Peter Galbraith, who was the U.N.’s deputy special representative for Afghanistan until the fall of 2009, told ProPublica that “an investigation would’ve required a push from the U.S. It required the cooperation of the coalition forces.” (Neither the U.N. mission in Afghanistan nor the office of the High Commissioner on Human Rights responded to our requests for comment.)

The mass grave at Dasht-i-Leili is one of many left unexamined in Afghanistan. In late 2011, the nation’s Independent Human Rights Commission concluded a massive report on decades of war crimes and human rights abuses, which reportedly documents 180 mass graves across the country. The region near Dasht-i-Leili is also believed to hold the remains of civilians massacred by the Taliban in 1998, in what Human Rights Watch called “one of the single worst examples of killings of civilians in Afghanistan’s twenty-year war.” In all, the report named 500 individuals responsible for mass killings – some of whom hold prominent government positions.

American and Afghan officials reportedly discouraged publication of the report, and the commission has still not made it public. “It’s going to reopen all the old wounds,” an American Embassy official told the New York Times last year. Afghanistan also recently adopted an amnesty law offering blanket immunity for past war crimes.

Nader Nadery, the commissioner responsible for the report, told ProPublica: “I haven’t seen any political or even rhetorical support of investigations into Dasht-i-Leili or any other investigation into past atrocities, from either Bush or Obama.”