Researchers of the Guatemalan Forensic Anthropology Foundation said 10 sets of human remains had been exhumed from the site.
The exhumations were done at the request of the National Commission of Guatemalan Widows, whose husbands and relatives were among the 200,000-odd people killed during the conflict.
A majority of the victims of the civil war were civilians.
The Commission believes that as many as 200 victims of American-backed military counter-insurgency raids could be buried at the former base in western Guatemala.
Most of the victims are believed to have disappeared from the nearby Indian village of Comalapa, 30 miles west of Guatemala City.
Fredy Peccereli, director of the Anthropolgy Foundation, said the skeletal remains bore signs of torture, with their necks and wrists bound by ropes and wires.
Guatemala's long and brutal civil war had pitted leftist guerillas against successive conservative governments, before ending in a peace accord in 1996.
US sided with Guatemalan army
In 1954 during the Eisenhower Administration, CIA support enabled a military junta to overthrow the left-wing regime. From that moment the Pentagon sided with a military that carried out some of the most brutal atrocities in South American history.
The Guatemalan army, backed by the CIA and US military, carried out brutal counter-insurgency campaigns, including genocide, kidnappings and killings, during the period.
Just before he left office, US President Bill Clinton apologised for what many saw as a dark and long-buried episode of America's foreign policy ... its support for brutal right-wing governments in Guatemala during a 36-year civil war in which 200,000 people died.
He said in March 1999: "For the United States it is important I state clearly that support for military forces and intelligence units which engaged in violence and widespread repression was wrong and the United States must not repeat that mistake."
It was the first time ever a US president had directly admitted the US role in that country's atrocities and took many human rights groups by surprise.
Intelligence documents which have since become declassified revealed vivid details of mass killings, kidnappings, torture and other horrors carried out by Guatemalan security forces trained and armed by the CIA and the US army.