The remains of the infant, believed to have been seven months old, were discovered on Tuesday on a peninsula in the Yunguyo region near the Bolivian border.
Investigators believe the killing may have been a ritualistic sacrifice to appease an ancient earth deity.
The body was surrounded by flowers, liquor bottles and containers of blood. Highland Indians consider many Andean hilltops to be the homes of earthen deities.
Peruvian anthropologist Juan Ossio said that human sacrifices date back to the Chavin culture, which flourished in Peru between 900-200 B.C.
"Sacrifices were made for more than a thousand years and it is hard to get rid of deeply rooted beliefs," he said.