The temple on the periphery the Sacsayhuaman fortress 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 believe 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. "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still waiting for carbon dating tests, but Camacho said their calculations about the facilities' age are supported by historical references such as ceramics and construction style.
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 in the next century.
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 some 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.
"The temple is one of the most important in the Sacsayhuaman site," Camacho said.
Part of the structure was destroyed by dynamite blasts in the early 20th century, when the site was used as a stone quarry.
The roadway, buried for hundreds of years under a meter (a yard) of soil, is believed to have formed part of a network connecting Sacsayhuaman's buildings, according to Camacho.
Archaeologists are also busy unearthing an advanced hydraulic system, which may have been used to supply water to Cuzco during the Inca empire.
The team believes the irrigation system was built by the Ayarmaca, who occupied the region from 900 to 1200. Remnants of Ayarmaca ceramics are scattered throughout the site.
The new excavations, directed by Cuzco's National Culture Institute, began in June 2007 and will continue for another five years, Camacho said.