Juan Emilio Cheyre, who tried to distance the military from the Pinochet regime when he commanded Chile's army from 2006 to 2006, faces several allegations of human rights abuses as a young officer during the coup, The Santiago Times reported.
He resigned as head of the electoral service this year because of allegations he kidnapped a young boy whose parents had been killed in the 1973 military takeover.
Natacha, Yelena and Marianela Monroy Rodríguez say they were 1, 3 and 8 in October 1973 when their home was raided by a group of soldiers led by Cheyre. Their father was already under arrest and the soldiers had come to arrest their mother.
"The raid was violent, they broke all the windows of the house, broke all the furniture," Yelena wrote in an open letter earlier this year.
She said the girls were told to stand against a wall and Cheyre ordered the soldiers guarding them to hit them with the butts of their guns if they moved.
The sisters were held in the women's detention center in La Serena until 1975.
Judge Jaime Franco at the Appellate Court of La Serena ordered their case to be investigated earlier this week.
In 2004, Cheyre wrote an essay, "Chilean Army: End of a Vision," in which he said human rights abuses cannot "be ethically justified." The essay acknowledged abuses during the rule of Pinochet, a career officer who was named army commander in chief by President Salvador Allende a month before the coup.
Pinochet, who died in 2006, governed Chile from 1973 to 1990.