The U.S. military has systematically covered up or disregarded “abundant and compelling evidence” of war crimes, torture, and unlawful killings in Afghanistan as recently as last year, according to a report by Amnesty International published today in Kabul.

The human rights organization alleges that the U.S. military has routinely failed to properly investigate reports of criminal behavior and, in some instances, tampered with evidence to conceal wrongdoing. On the rare occasions when servicemen are held to account, the report found that the compromised military justice system seldom secured justice for the victims of enforced disappearances, killings, and abuse that included torture.

“President Obama has admitted that ‘we tortured’ people in the past—but this is not the Bush administration, this is torture happening under Obama,” said Joanne Mariner, the author of the report.

While torture and other abuses by the CIA and the military were sanctioned by the Bush administration, Obama entered office vowing to end such practices. There have been a number of prosecutions and punishments of military units that have committed crimes and atrocities in Afghanistan under Obama, but Amnesty says the White House has to do more to ensure his policy changes are respected in the field.

A survivor of one of the most egregious assaults on civilians detailed in the report told The Daily Beast he had been forced to listen to the last gasps and sobs of his dying daughter, who was seven months pregnant, while the Americans threatened to kill anyone who moved. “She was calling out for help, maybe she wanted to share her last words before she left us forever,” said Muhammad Tahir, a civil servant.

Four years after two pregnant women, two criminal justice officials, and a teenage girl were shot dead during a party to mark the birth of a grandson in Khataba Village, Paktia Province, Tahir and his family are still waiting to be interviewed as part of an investigation the U.S. military promised to carry out.

“There is a shocking lack of accountability for the killing of Afghan civilians by U.S. forces, including civilians killed in circumstances that raise concerns about war crimes,” said Mariner. “There is very strong evidence that war crimes were carried out.”

The report, titled “Left in the Dark,” includes detailed investigations of 10 incidents in which at least 140 civilians, including 50 children, were killed in dubious circumstances. In the aftermath of nine of these, eyewitnesses and families report that no one was ever interviewed by the U.S. military.

A Pentagon spokesman did not deny the allegations in the report but reiterated U.S. policy on torture and war crimes. “The Department of Defense does not permit its personnel to engage in acts of torture or cruel, inhuman, or degrading treatment of any person in its custody,” said Maj. Bradlee Avots.

According to the Amnesty report, a Special Forces unit had raided the house on February 12, 2010. Five people were killed, some by sniper fire, some at closer range. When the Americans realized that the pregnant women and children they had killed were unlikely to be insurgents, witnesses said they began to remove the evidence of what they had done.

“When they understood they had hit the wrong place, they started pulling out the bullets from the dead bodies with their hands and their knives,” Tahir recalled. “America, the killer nation, we will never forgive you.”

The day after the assault, ISAF announced that forces had stumbled upon the dead women after a firefight with insurgents. In the following days they would go on to brief the press with a series of lurid but inaccurate stories suggesting that there was evidence of honor killings or execution-style murders.

“The immediate effort to cover up what had been done suggested that they realized it was a crime,” said Mariner. “And the changing story over time definitely suggests a cover-up.”

Amnesty says Tahir’s family is just one of thousands who have waited in vain for justice for their missing, dead, or severely injured loved ones. Foreign forces in Afghanistan have immunity from local prosecution, leaving the U.S. military itself, under the Uniform Code of Military Justice, to investigate and try American troops when they are accused of criminal acts.

Among the most disturbing allegations are claims of forcible disappearance, torture, and extrajudicial killings carried out by a rogue unit in Wardak province from the fall of 2012. “We interviewed a former detainee that had a really horrific story of just raw torture,” Mariner said. “It’s not only the testimony of this former detainee but a lot of bodies were found showing horrendous crimes of torture—people missing body parts and people whose corpses were badly mutilated.”

One of 125 victims and eyewitnesses interviewed by Amnesty in compiling this report was Qandi Agha, 51, an employee at the provincial Ministry of Culture, who says he was captured by U.S. forces who broke into his home and spirited him away to a dark wooden cell. “On the first night,” he said, “the Americans told me they were going to try 14 different types of torture on me. If I survived, they said, they’d let me go.”

He said he suffered electric shocks, beatings, simulated drowning, hanging from the ceiling, partial burial in freezing conditions, and the extraordinary and degrading torment of having a length of string tied tightly around his penis. “They left the string around my penis for four days. My abdomen was bulging. I wasn’t able to pee for those four days,” he said.

He was lucky. He says half of the men he was incarcerated with did not survive the ordeal, and he claims to have watched one man be beaten to death by a redheaded American commando.

The U.S. authorities first became aware of allegations against the Special Forces team operating out of Combat Outpost Nerkh in December 2012. The American-led miliary coalition denied the charges of abuse. But by February 2013, the allegations had become so vehement that the Afghan president, Hamid Karzai, ordered Special Forces to leave the province.

“The U.S. knew about complaints, and that obviously raises concerns as to why this wasn’t stopped sooner, because the abuses went on. There were people who were disappeared as late as February” in 2013, said Mariner.

Amnesty says relying on an internal justice system is not conducive to thorough investigations of alleged crimes; the commanders whose duty it would be to report incidents may be implicated, and there is a heavy reliance on the word of the accused and their colleagues rather than independent witnesses.

The military insists that civilian deaths are investigated whenever allegations of unlawful killing are made. “In accordance with standard practice, the United States has investigated U.S. military personnel and civilian personnel, including contractors, for civilian casualties that are alleged to be not incident to lawful military operations. Investigation results can and have previously led to both criminal convictions, as well as adverse administrative actions,” said Avots.

For Tahir, who lost his pregnant daughter, and many more like him, those words will ring hollow.

“We lost five members of the family and about 20 kids became orphans,” he said, in a tearful phone interview. “What was our crime? Can the Americans tell us?”