They had been carrying out conservation work on the site on behalf of Peru’s Ministry of Culture when they came across the remains, which had been obscured by sand and rocks.
The walls would have been 2.5m (8ft) high, but only about 70cm remain with the hearth at the centre
They said the temple walls were made of stone and covered in fine yellow clay which also contained some traces of red paint.
The archaeologists said the find suggests that the communities in the Late Pre-ceramic Age (3500 BC to 1800 BC) were more closely connected than had been previously thought.
Story: BBC News | Photo: Peruvian Ministry of Culture