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.