The mud statuettes were found inside a reed basket in a building at the ancient city of Vichama in northern Peru, which is today an important archaeological site.
The ministry said yesterday they were probably used in religious rituals performed before breaking ground on a new building.
Two of the figures, a naked man and woman painted in white, black and red, are believed to represent political authorities. The third, a women with 28 fingers and red dots on her white face, is believed to represent a priestess.
The Caral civilisation emerged some 5,000 years ago and lived in Peru's Supe Valley, leaving behind impressive architecture including pyramids and sunken amphitheaters.