The discovery, dubbed the Temple of Fire, was found in one of the wings of El Paraiso's main pyramid. It includes a hearth that experts believe was used to burn ceremonial offerings.
"The smoke allowed the priests to connect with the gods," said Marco Guillen, who led the team of researchers who made the find.
Archeologists found the hearth in mid-January as they were carrying out conservation work at a set of 4,000-year-old ruins known as El Paraiso, located some 40 kilometers northeast of Lima in the Chillon River Valley.
The discovery shows "that the Lima region was a focus of civilizations in the Andean territory," Deputy Culture Minister Rafael Varon told reporters.
Archeologists believe the ancient coastal civilizations raised crops including cotton, which they traded with coastal fishermen for food.
El Paraiso, spread across 50 hectares (125 acres), has 10 buildings and is one of the largest ancient sites in central Peru.