By David Jolly
KABUL, Afghanistan — A series of home raids by C.I.A.-trained Afghan counterterrorism forces in the last month resulted in the deaths of at least six innocent civilians, according to Afghan government officials, reviving an issue that has been a chronic source of tension between Afghanistan and the United States.
The deaths happened over the course of three raids in the restive eastern province of Khost, the officials said, including a Nov. 20 episode in which a husband and wife were killed with two American advisers present. The raids were conducted by the Khost Protection Force, one of the regional units known as counterterrorism pursuit teams, set up by the C.I.A. to fight the Taliban, the Haqqani network and Al Qaeda.
The C.I.A. has trained thousands of Afghan forces for such missions — around 3,500 in the Khost Protection Force alone. But from the start, some senior Afghan officials have considered them a problem, accused of human rights abuses and seen as largely unaccountable.
The C.I.A. began dismantling or shrinking the teams as the agency began a partial withdrawal from Afghanistan in recent years. And control of the pursuit teams was officially shifted to the Afghan intelligence agency, the National Directorate of Security, from the C.I.A. two years ago, at the request of Afghan officials.
But some now say the remaining Afghan counterterrorism forces are still largely unaccountable to the government.
One former senior Afghan government official, who spoke on the condition of anonymity to discuss intelligence issues, said that the transfer of authority in some cases had not been completed. “The main problem is that there are a number of people working for the C.I.A. who will not work for the Afghan armed forces,” the former official said.
There are also concerns about former members of the teams who were paid a $2,000 severance and dismissed by the C.I.A. “That could cause problems for us in the future,” the former official said, particularly if those highly trained people were to end up on the wrong side of the law.
The National Security Directorate did not reply to requests for comment, and officials in the office of President Ashraf Ghani did not immediately reply to requests for comment on Wednesday. A C.I.A. spokesman declined to comment.
One American official, speaking on the condition of anonymity to discuss a classified security force, defended the Khost pursuit team as “one of the most effective elements fighting the Taliban in Afghanistan.”
The official added, “This is a group made up of thousands of soldiers who come from the area and consequently have the respect and insights necessary to operate in a professional manner despite the constant engagement with the enemy.”
Khost has long been a critical battlefield, as it is a strategic gateway for Taliban and the Haqqani network to bring fighters into Afghanistan from their havens in the Pakistani tribal areas across the border. It is also a crucial corridor to Kabul, and American and Afghan officials have long felt that gains by the Taliban there could pose a threat to the capital.
In the latest militant attack in Khost, a roadside bomb attack on Wednesday apparently aimed at Habib Khan Taniwal, a member of the provincial council, killed two people and wounded seven others, including three of his bodyguards, officials in the province said. Mr. Taniwal survived.
The first Khost Protection Force raid under scrutiny happened on Nov. 7 in the Dery neighborhood of the provincial capital, Khost City. Operatives arrived in pickup trucks and raided a home there, killing a 45-year-old man and his 17-year-old nephew — both described as innocent civilians by Abdul Wahed Patan, deputy to the Khost governor.
About 1,000 people protested those killings, trying to carry the bodies of the two victims to the regional capital, according to people who participated in the demonstrations. They were stopped en route by the counterterrorism force and told to go back or face a possible assault by American troops, they said. The protesters went home.
In another raid in Khost City, on Nov. 11, a 50-year-old man and his 26-year-old son were wrongfully killed, according to Mr. Patan and the district governor, Jawid Joshan.
In the Nov. 20 raids, the Khost force, accompanied by two American advisers, arrived by helicopter around 1:30 a.m., dismounted and raided three houses in the district of Zazi Maidan, according to General Azizullah, the district police chief.
One of the houses belonged to a recently discharged Afghan Army soldier named Ibrahim Jan. Neighbors said that Mr. Jan had heard noises and ran outside with his assault rifle to protect his family. Members of the counterterrorism force had climbed onto his roof, and shot and killed him before he fired. When his wife ran out to him, they gunned her down, too, the neighbors said.
It is not unusual for Afghans to be armed, and the police in Khost have often allowed some at-risk people to carry weapons for personal protection. As a former soldier, Mr. Jan would most likely have feared being singled out as a target by the Taliban.
At another house in Zazi Maidan, belonging to a man named Mia Gul, the Khost Protection Force seized weapons and detained two men, Mr. Gul and his brother Rahmat Gul, and took them to the Camp Chapman base nearby, local officials said. Mia Gul was released the next morning, but Rahmat Gul remains in custody.
Home raids have long been a source of outrage — and civilian casualties — for Afghans, and in 2013 American commanders sharply limited them at the demand of former President Hamid Karzai.
But even after the formal end of the NATO combat mission last year, such raids have again become common. American officials have described them as a crucial weapon against militants, but the raids are still a source of concern when they come to light.
“As long as the so-called U.S. war on terror is unwisely conducted in the Afghan villages and towns, there will certainly be civilian casualties,” said Aimal Faizi, who served as spokesman to Mr. Karzai and has been a critic of Mr. Ghani’s government.
“It is the responsibility of the Afghan government to protect its citizens,” he added, “but the national unity government seems to be disregarding cases of civilian casualties in Afghanistan involving U.S. forces.”
Ashley Jackson, a former United Nations official in Kabul and now a research associate at the Overseas Development Institute in London, said that with the transition to Afghan-led forces, the actions of shadowy units like the counterterrorism pursuit teams are harder to examine. “There’s less and less accountability,” she said. “There’s less Western focus, and fewer people care.”
Farooq Jan Mangal contributed reporting from Khost Province, Rod Nordland from Kabul, and Mark Mazzetti from Washington.