January 01, 2019 "Information Clearing House" -     NADER SHAH KOT, Afghanistan — Razo Khan woke up suddenly to the sight of assault rifles pointed at his face, and demands that he get out of bed and onto the floor.

Within minutes, the armed raiders had separated the men from the women and children. Then the shooting started.

As Mr. Khan was driven away for questioning, he watched his home go up in flames. Within were the bodies of two of his brothers and of his sister-in-law Khanzari, who was shot three times in the head. Villagers who rushed to the home found the burned body of her 3-year-old daughter, Marina, in a corner of a torched bedroom.

The men who raided the family’s home that March night, in the district of Nader Shah Kot, were members of an Afghan strike force trained and overseen by the Central Intelligence Agency in a parallel mission to the United States military’s, but with looser rules of engagement.

Ostensibly, the force was searching for militants. But Mr. Khan and his family had done nothing to put themselves in the cross hairs of the C.I.A.-sponsored strike force, according to investigators.

It was clear that the raiding force had “committed an atrocity,” said Jan-mir Zazai, a member of the Khost provincial council who was part of the government investigating team. “Everyone we spoke to said they would swear on the innocence of the victims.”

At a time when the conventional Afghan military and police forces are being killed in record numbers across the country, the regional forces overseen by the C.I.A. have managed to hold the line against the most brutal militant groups, including the Haqqani wing of the Taliban and also Islamic State loyalists.

But the units have also operated unconstrained by battlefield rules designed to protect civilians, conducting night raids, torture and killings with near impunity, in a covert campaign that some Afghan and American officials say is undermining the wider American effort to strengthen Afghan institutions.

Those abuses are actively pushing people toward the Taliban, the officials say. And with only a relatively small American troop contingent left — and that perhaps set to drop further on President Trump’s orders — the strike forces are increasingly the way that a large number of rural Afghans experience the American presence.

Many of the strike forces were officially put under the control of Afghan intelligence starting in 2012. But senior Afghan and international officials say that the two most effective and ruthless forces, in Khost and Nangarhar Provinces, are still sponsored mainly by the C.I.A.

Those fighting forces, also referred to as counterterrorism pursuit teams, are recruited, trained and equipped by C.I.A. agents or contractors who work closely with them on their bases, according to several current and former senior Afghan security officials, and the members are paid nearly three times as much as regular Afghan soldiers.

The Afghan ownership of those two units is only nominal, a liaison relationship in which intelligence headquarters in Kabul has representatives on the mission for coordination. But the required pre-approval for raids is often last-minute, or skipped until afterward, the officials say.

For months, The New York Times has investigated the human toll of the C.I.A.-sponsored forces on communities. Times journalists researched frequent complaints — at times almost weekly — that these units had raided and killed civilians, and The Times went to the sites of half a dozen of their raids, often less than 24 hours after the force had left.

The investigation found details of a C.I.A. mission with tactical successes that have come at the cost of alienating the Afghan population. One former senior Afghan security official bluntly accused the strike forces of war crimes.

Often, the raids that resulted in civilian deaths were carried out not far from police outposts or government offices, leaving those American-supported officials humiliated in the villages they had been trying to establish relationships with. And because the C.I.A.-sponsored units often use English during operations, their abuses are even more directly equated with the American presence, though claims that American agents have sometimes been on the missions have not been confirmed.

“The dilemma is this: The C.I.A. needs to fight its wars in the shadows,” said Karl Eikenberry, a former commander of American forces in Afghanistan who later served as the United States ambassador to Kabul. “But when the U.S. also takes on the mission of state-building, then the contradictions between the two approaches — stealth, black ops, and non-transparency vs. institution building, rule of law, and accountability — become extraordinarily difficult to resolve, and our standing as a nation suffers.”

United Nations reports have expressed concern about civilian deaths and “consistent, credible accounts of intentional destruction of civilian property, illegal detention, and other abuses” by the units. The United Nations said the forces in Khost, in particular, operated outside the Afghan government’s structure “with an absence of transparency and ongoing impunity.”

In the village of Nader Shah Kot, the provincial official who helped investigate the raid, Mr. Zazai, said the force’s impunity was alienating residents from the government and increasing support for the Taliban.

“If there had been arrests, if there had been justice, this wouldn’t continue like this,” Mr. Zazai said. “But there is absolutely no justice.”

American defense officials in Washington say the C.I.A. operations in Afghanistan are largely opaque to military generals operating in the war zone. The C.I.A.’s level of partnership has been declining as the Afghan intelligence agency and its forces grow more mature, the officials said. But as American military forces are set to draw down, the role of the Central Intelligence Agency is only likely to grow in importance.

A spokeswoman for the C.I.A. would not comment, nor would Afghans directly involved with the forces. Afghan security officials in Kabul tried to play down the level of the forces’ autonomy and the nature of their abuses. When pressed with details of specific cases, they did not respond.

The number of casualties varied among the cases The Times investigated. In one, two brothers were killed as they watered their fields before dawn after receiving permission from the local security outpost. In another, a unit pursuit of a Taliban target went into the wrong house in Laghman Province and killed 12 civilians, officials there said.

One of the most gruesome episodes examined by The Times was in Khogyani District, in Nangarhar Province. The forces handcuffed and hooded two brothers and, after a brief interrogation as their wives and children watched, both men were dragged away and executed in a corner of a bedroom that was then detonated over their heads, according to relatives and villagers who pulled the bodies out of the rubble.

When Times journalists arrived at the house 16 hours after the raid, the area was a scene of carnage with burned vehicles and crumbled walls. The family’s patriarch, Hajji Hassan Jan, 60, said that a security outpost overlooked their house, and that the district’s intelligence chief, who was a regular guest for dinner, had no answer for why the house was raided and his sons killed.

Still, he tried to guess: It was probably for feeding the Taliban. In rural Afghanistan, traditions of hospitality demand that you feed whoever knocks at your door. When those men are armed, there is little choice.

“The forces once asked my son, ‘Why do you feed the Taliban — why cook chicken for them, or bring them yogurt?’” Mr. Jan said. “My son told them: ‘We made chicken for them. If you come, we will make an entire lamb for you.’”
Rooted in Counterterrorism

The origin of C.I.A.-sponsored strike forces in Afghanistan was in the early days of the American invasion in 2001, when the United States allied with militia forces to help topple the Taliban regime.

Once the Taliban and Al Qaeda started fleeing, often across the border into Pakistan, there was no organized Afghan force to create the needed lines of defense.

In the eastern province of Khost, largely under the influence of the Haqqani network, which had strong ties to Al Qaeda, the C.I.A. started organizing local militias into a force that could strike at insurgents as they tried to come in or out.

Men from the Bati Kot district of Nangarhar gathered on June 1 to pay respects after four members of a family were killed in a raid by the C.I.A.-sponsored strike force.CreditJim Huylebroek for The New York Times

“These forces were created in border areas at first to stop Al Qaeda fighters,” said Ghaffar Khan, a Czechoslovakia-trained police officer from Soviet times whom the C.I.A. had recruited as one of the force’s first commanders.