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 3year-old daughter, Marina, in a corner of a bedroom that had been set on fire.
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. The strike force has 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 crosshairs 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’s 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 Islamic State loyalists. But the units have 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 small American troop contingent left — and that set to drop further on President Trump’s orders — the strike forces are increasingly the way that some 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 the agency on its bases, according to several current and former senior Afghan security officials. The fighters 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, the Afghan capital, has representatives on the mission for coordination. But the required approval for raids is often given at the 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 Afghan communities. The 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 strike force had left.
The investigation found details of a C.I.A. mission with tactical successes, but 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. The raids that resulted in civilian deaths were often carried out near police outposts or government offices, leaving 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.”
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 Nader Shah Kot, the provincial official who helped investigate the raid on Mr. Khan’s home, 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 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 have grown more mature, the officials said.
But as American military forces are set to draw down, the role of the Central Intelligence Agency is 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.
C.I.A.-sponsored strike forces in Afghanistan began 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 of the country.
It was meant to be a stopgap program. But the force proved so effective, even after the Taliban began attacking the government and the Americans, that it expanded to other parts of the country. In Khost, the so-called protection force was consolidated and based out of Camp Chapman, the main C.I.A. outpost there. The unit in Khost still has the largest number of fighters: Officials put the number anywhere from 3,000 to more than 10,000. It patrols border areas and runs its own network of informants.
Several current and former Afghan officials said that the C.I.A. still largely commanded the strike forces in Khost and Nangarhar, effectively putting the units above the law. American agents and contractors work closely with the strike forces on their bases, developing targets and helping guide operations from headquarters.
And the Americans have a presence at bases where detainees have accused the units of torture and abuse, officials say. In a period of a little over a year, human rights officials registered at least 15 complaints of torture by the strike force based in Nangarhar Province, which has roughly 1,000 fighters and is known as “02.” At a September news conference in the city of Jalalabad, elders from three districts of Nangarhar said that over 100 civilians were killed by the 02 unit the month before. (That number could not be verified independently.) “Before the people start protests, before the people pick up weapons against the government, the government needs to rein in these kind of reckless operations,” said one tribal elder, Malik Zaman.