With 10 ruins, El Paraiso is one of the most extensive archaeological sites in central Peru.
Researchers said they made entry into the 22-foot by 26-foot rectangular structure of the temple by way of a narrow passageway, and found a hearth at its center they believe was used to burn ceremonial offerings.
The temple was the first structure of its kind to be found on Peru's central coast, they said.
"It corroborates that the region around Lima was a focus for the civilizations of the Andean territory, further bolstering its religious, economic and political importance since times immemorial," Peru's Deputy Minister for Culture Rafael Varon said.
The hearth gave clues about the civilization that had used the site, researchers said.
"The main characteristic of their religion was the use of fire, which burnt in the center," archaeologist Marco Guillen, leader the team making the discovery, told the BBC.
"The smoke allowed the priests to connect with their gods," he said.
The Paraiso settlement, consisting of both a farming and fishing community, would have sustained hundreds of people, the researchers said.