The temple on the periphery of the Sacsayhuaman fortress casts added light on pre-Inca cultures of Peru, showing that the site had religious as well as military aims, according to researchers.
It includes 11 rooms thought to have held mummies and idols, lead archaeologist Oscar Rodriguez told The Associated Press.
The team of archaeologists that made the discoveries believes the structures predated the Inca empire but were then significantly developed and expanded.
"It's from both the Inca and pre-Inca cultures; it has a sequence," Washington Camacho, director of the Sacsayhuaman Archaeological Park, told the AP on Thursday. "The Incas entered and changed the form of the temple, as it initially had a more rustic architecture."
Archaeologists are still waiting for carbon dating tests, but Camacho said their calculations about the facilities' age are supported by historical references such as ceramics and construction style.
Previous carbon-14 dating of Sacsayhuaman revealed that the Killke culture constructed the fortress in the 1100s, said Peruvian archaeologist Luis Lumbreras, former director of Peru's National Culture Institute and an expert on Cuzco's pre-Incan cultures. He was not involved in the dig.
The Killke occupied the region from 900 to 1200 A.D., prior to the arrival of the Incas.
"These recent discoveries add to our knowledge of Sacsayhuaman, confirming again the aggregate nature of the fortress," Lumbreras told The Associated Press.
The Inca empire, based in the ancient city of Cuzco, flourished along the western edge of South America during the 1400s, prior to the arrival of the Spanish.
Today, Cuzco is Peru's main tourism hub and a launching point for visitors to the jungle-shrouded ruins of Machu Picchu, 40 miles northwest.
The temple lies a little under a mile from zigzagging walls of the Sacsayhuaman fortress, alongside an enormous rock formation believed to be one of the fortress' burial mounds.