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.

“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.

It was meant to be a stopgap program. But the force proved so effective, even after the Taliban started coming hard at the government and the American presence, that it kept expanding 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, though the exact count is unclear: Officials put the number anywhere from 3,000 to over 10,000. It patrols border areas and also runs its own network of informants.

Commander Ghafar said he believed the forces remained necessary, otherwise the defense against Haqqani-run suicide bombers would buckle, making it easier for attackers to reach Kabul. On the other hand, he said, their abuses were taking a toll.

Former President Hamid Karzai spent years trying to rein in American forces from carrying out night raids that angered villages and set them against his government, only to realize that the C.I.A.’s Afghan forces were doing the same.

One episode in particular made Mr. Karzai furious. In 2009, the strike force in Kandahar tried to forcibly release one of its colleagues detained by the police on criminal charges. When the most senior law enforcement official in the province, Gen. Matiullah Qateh, resisted, he and several of his officers were shot dead, former and current Afghan officials say. The C.I.A. reluctantly surrendered the guards involved in the killing of the general, after the Afghan leadership threatened to use force.

Mr. Eikenberry, the former general and ambassador, said the C.I.A.-sponsored forces “which operated outside of the framework that governed those under sovereign control of the Afghan government” raised concerns from the beginning.

“But Bin Laden was not yet found, Al Qaeda was active in the border areas, and Afghanistan did not have forces capable of dealing with what was regarded as an existential threat to the U.S. So the concerns never led to action,” Mr. Eikenberry said. “The problem was one to be solved later in the campaign, so to speak. And the C.I.A. was the dominant voice in the chamber.”

A Surge of Abuse

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 them on their bases, develop the targets for them, and help guide the 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.

Mohammed Taher, from Khogyani District, said he and two of his brothers were detained in a night raid last spring. He was held for three months and five days, about a week of it at the air base in Nangarhar where the strike force is based.

“They said, ‘We will drive a tank over you if you don’t say your brothers are Taliban.’ I said, ‘If you have evidence that they are, show me,’” Mr. Taher said. “They wanted me to say all that so they could take a video of me saying it.”

Mr. Taher said Americans were present during the raid when he was detained, but he did not see Americans during the questioning and the torture at the base. His mistreatment stopped when he was handed over to the regular Afghan intelligence force, he said.

“My hands were cuffed. They punctured these veins with needles and blood was running,” he said.

Sabrina Hamidi, who leads the Afghan Human Rights Commission in the east, said that during her 13 years of work at the commission she could not recall a single example of access to the regional forces to examine accusation of abuses.

“In their operations, most of the times the harm to civilians is direct,” Ms. Hamidi said about the 02 unit. “When they make arrests, there is usually torture involved, also.”

In nearly every case examined by The Times, the victims’ families said they were at a loss for where to seek justice, or an explanation of why they had been raided. And nearly every government official in those areas expressed helplessness about the strike forces’ operations.

‘I Thought It Was the Caliphate’

In the Bati Kot district of Nangarhar Province, the strike forces conducted a raid in May, leaving their headquarters at the air base in Jalalabad and arriving in a convoy of several dozen vehicles at a village surrounded by corn fields and orange orchards.

One resident, Khoshal Khan, who works at a medical university, thought at first that the raid was an attack by the Islamic State.

“I ran and got my weapon — I thought it was the caliphate people. I didn’t know it was the government,” Mr. Khan said. “Then they started firing, and I heard the gate blown up. They were speaking English, also.”

Families often sleep outside because of the heat. One family patriarch, Mohamed Taher, in his late 50s, was shot near his bed on the roof.

When Times journalists arrived the day after the raid, the bed was broken, the mud roof under the bed patched with blood, just steps from dried tomatoes sunning on a tarp.

One of Mr. Taher’s grandsons, Sekandar, 16, was visiting from Jalalabad during a school break. He was sleeping in the yard and was awakened by gunshots, he said, spotting the light from the raiders’ laser sights racing around. Sekandar said the forces spoke both Pashto and English.

The strike force had climbed ladders and was on the walls of the house, ordering Mr. Taher’s family to come out. But Sekandar said that when they followed the order to come out with their hands up, one of Mr. Taher’s sons, Naeem Shah, was shot in his left hand. Then a grandson, Shaker Khan, was shot in the head.

“The women started crying. They called to be quiet, then they blew up the gates and came in,” Sekandar said. His account matched those of other family members and neighbors.

Another of Mr. Taher’s sons, Mohammed Raheem, had also been gunned down. The remaining men were handcuffed, and the women and children were put in one room.

Before the forces started leaving about two hours later, with Naeem Shah still wounded, the fighters warned the family not to come out for an hour after they had left, said Mr. Shah’s young son, Adel, 10.

“They said, ‘Don’t come out — if the airstrikes hit you, then don’t complain,’” said Adel, whose face had shrapnel wounds from the raid. While the family waited in the house, Adel’s father bled to death in the yard.

The district governor’s office is just 100 yards from the house, and there are two police outposts nearby.

Mohibullah, a relative of the dead, said that for him, there was no difference between the C.I.A.-sponsored force and the Islamic State if the result was to be attacked with no warning.

“What is the need for raiding me at night?” he said. “Send me a warrant. If I didn’t show up, then you can bring your tanks and fly your planes and destroy me.”