The court handed former army chief of staff General Benedicto Lucas a 33-year term for crimes against humanity over the aggravated rape of Emma Guadalupe Molina Theissen at a military barracks.

Three other officers, Manuel Callejas, Hugo Zaldana and Francisco Gordillo, received the same sentence.

The three judges handed Lucas, Zaldana and Callejas an additional 25 years for the disappearance of her Emma Guadalupe's brother, Marco Antonio Molina Theissen.

A fifth officer, Edilberto Leton, was found not guilty.

Marco Antonio, aged 14, was kidnapped from his family home by a group of soldiers in the capital of the Central American country on October 6, 1981, and is still missing.

The abduction came a day after his sister, then 21, escaped from a military barracks in the west of the country where she had been tortured and repeatedly raped.

Dozens of activists, who waited almost 14 hours to hear the sentence, applauded, embraced and cheered, while relatives and friends of the accused shouted slogans in support of the officers and sang the army anthem.

Emma Guadalupe appealed to the accused toward the end of the trial to "have a bit of honor and tell us where Marco Antonio is."

The officers were arrested in January 2016 and a judge ordered their trial last year.

Lucas, brother of the late president Romeo Lucas (1978-1982), watched Wednesday's ruling by video-conference from the military hospital where he is being held.

He is also facing prosecution, along with seven others, by another court for his alleged participation in at least 88 massacres of indigenous people during the 1960-1996 civil war.

The war between government troops, left-wing rebels and right-wing vigilante groups left an estimated 200,000 people dead or missing, according to the United Nations.