BOGOTÁ, Colombia — A special court in Colombia has charged a general and other top military leaders of crimes against humanity, accused of assassinating 120 civilians and presenting them as combat casualties in a bid to show the country was winning its long civil war.

The indictments are the first in which Colombia’s special peace court, created by a 2016 agreement between the country’s government and its largest rebel group, has held anyone accountable for the killings, which erupted into public view in 2008 and became known as the “false positives” scandal.

The scandal has emerged as emblematic of the country’s decades-long internal conflict, a painful symbol of the way civilians were not just accidental casualties in a war between left-wing guerrillas, paramilitaries and the military — but sometimes targets of all three groups.

Hundreds of members of the military were convicted in the scandal by the country’s regular court system but were later released under the 2016 peace accord, which transferred jurisdiction of their cases to the special peace court.

Tuesday’s indictment is notable, said Juan Pappier, Colombia researcher for Human Rights Watch, in that it holds several high-ranking individuals accountable. Past indictments in the regular court system focused on lower-ranking officials.

Among the 11 people indicted by the peace court are Brig. Gen. Paulino Coronado Gámez and the colonels Santiago Herrera Fajardo and Rubén Darío Castro Gómez.

The indictment said the killings, which took place in 2007 and 2008 in the Catatumbo region, near the border with Venezuela, “were not isolated, spontaneous or sporadic acts.”

Instead, the indictment said, “these acts are interrelated and were committed as part of a widespread and systematic attack against the civilian population, that is, they are crimes against humanity.”

Mr. Pappier called the announcement “a vindication for victims and human rights groups that have been fighting for justice in this case for more than a decade.”

In February, the special peace court said that the military was responsible for killing as many as 6,402 civilians and trying to pass them off as combatant fatalities. Court officials said they will issue more indictments in the future.

Under the terms of the special peace court, the 11 individuals have the option to acknowledge the crimes as charged, or go to trial. If they admit to the crimes, they will receive up to eight years of an alternative sentence such as house arrest or labor. If they choose to go to trial and are found to be guilty, they could face up to 20 years in prison.

Many of the victims in Colombia’s false positives scandal came from poor neighborhoods. Blanca Nubia Monroy’s 19-year-old son, Julián Oviedo Monroy, disappeared one night in 2008 after he told his mother he’d been recruited for a job.

In an interview last year, Ms. Nubia Monroy, 62, said that she later discovered that the recruiters had handed him over to the military, who had killed him and tried to pass him off as a member of one of the country’s left-wing guerrillas.

On Tuesday, she said the indictment brought her a measure of peace. “They’re not going after the low-level officers like the regular justice system,” she said of the peace court. “They’re going after the highest ranks,” she added, “so that the deaths of our children do not end with impunity.”

Reported was contributed by Sofía Villamil in Cartagena.

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