Guatemala City – Guatemalan judges have unanimously ruled that the country’s military carried out genocide and crimes against humanity, but in a 2-1 decision acquitted former intelligence chief Jose Mauricio Rodriguez of all charges.

According to the decision, handed down late on Wednesday, there was no evidence Rodriguez was involved in or ordered others to take part in the genocide during the country’s decades-long armed conflict.

Over the course of the war, which began in 1960 and formally ended in 1996, more than 200,000 people were killed and another 43,000 were forcibly disappeared. More than 80 percent of the victims were indigenous Maya people. The worst of the atrocities took place in the Maya Ixil region, 225km northwest of Guatemala City.

“Inhuman acts were committed against the civilian population,” said tribunal president Maria Eugenia Castellanos.

“We are moved,” she added, referring to the countless survivors’ testimonies of military forces carrying out killings, massacres, rape, theft of children, bombing, displacement and forced starvation.

Dissenting judge

Rodriguez, along with former dictator Efrain Rios Montt, was accused of carrying out the massacre of nearly 1,800 Ixil civilians and disappearing tens of thousands others from March 23, 1982, through July 31, 1983.

Judge Sara Yoc, the dissenting vote on the Rodriguez ruling, said the former military intelligence commander absolutely would have known that the military was carrying out genocide and crimes against humanity. His role was to monitor and supervise intelligence-gathering from all regions, including information gathered through torture, she added.

“To me, [Rodriguez] is responsible for genocide,” Yoc said.

Former Intelligence chief Jose Mauricio Rodriguez greets supporters after being acquitted of committing genocide [Jeff Abbott/Al Jazeera]

Wednesday’s verdict came five years after Rios Montt, who seized power during the 1982 military coup, was convicted of genocide and crimes against humanity. Rodriguez was acquitted at the time.

But those verdicts were swiftly overturned by the country’s Constitutional Court, setting up a repeat of much of the trial, which began last October. Rios Montt, who was deemed unfit for court appearances or prison due to his dementia, died at the age of 91 last year.

Prior to Wednesday’s verdict, Rodriguez denied any involvement.

“I am sure that I am innocent,” he told the court. “I did not do or order others to do all the things it’s said happened.”

‘A crime was committed, but no one is responsible’

Following the verdict, genocide survivors filed out of the building to applause and chants of “yes, it was genocide” from those gathered outside.

Edwin Canil, the president of the Association for Reconciliation and Justice (AJR), said despite the not guilty verdict in Rodriguez’s case, the determination that genocide did occur is key.

“It’s huge for this country,” Canil told Al Jazeera, adding that the AJR will discuss how to seek justice.

A man holds his head in his hands as the court reads their decision to acquit former intelligence chief Jose Mauricio Rodriguez [Jeff Abbott/Al Jazeera]

At the same time, Canil sees the full ruling as somewhat contradictory, in that genocide was confirmed but no one has been convicted.

“A crime was committed but no one is responsible,” he said, describing the tribunal’s verdict.