It is unclear whether the cases at the three schools are related. But the prevalence of systematic sexual abuse of boys in Afghanistan has been a problem for generations. Bacha bazi — it means boy play — is common among men in powerful positions who keep boys as sex slaves. Bacha bazi boys are forced to dress as girls and to dance for men before being raped. Sometimes the boys are prostituted to the highest bidder.

In an interview with The New York Times this month, Mr. Musa said that his group — the Logar Youth, Social and Civil Institution — began intensively investigating after a troubling Facebook post in May that showed men with boys in sexual positions. One video provided by the group shows a teenage boy dancing barefoot for about two dozen men who stand or sit in a circle around him.

The post came down quickly, Mr. Musa said, but the group was able to preserve many of the images. Some of the boys were recognizable, and had complained of sexual abuse before, he said.

The Logar group began methodically talking to students in the area, finding dozens who said they had been raped. Many of their accounts were confirmed by teachers or other people in the area, who along with four of the boys were also interviewed by The Times.

As the accounts unfolded, at least seven boys who said they had been raped were found dead, Mr. Musa said, most likely at the hands of their own families.

Mr. Musa said that the advocacy group took the boys’ statements to Logar provincial police, but that no action was taken. He said several boys who had agreed to be questioned by the police were subsequently raped by officers.

Shapoor Ahmadzai, a spokesman for the Logar provincial police, said the accusations were false. “Nobody has come to the police for rape cases,” he said. “It’s just rumors.”