The mummies - of an adult and a child - were found at an ancient religious complex which has been under excavation since 1981.
The child is believed to have been an offering to the gods and may have been buried alive after the adult's death.
Researchers also found other offerings including the remains of guinea pigs and jars with feline designs.
"This is one of the most important finds in more than three decades of excavation, because the mummies are intact," researcher Gladys Paz told the AFP news agency.
The mummies are squatting and are fully dressed wrapped in rope.
It is the third intact find among more than 70 tombs uncovered in the Huaca Pucllana tomb, a pyramid-like temple built by the pre-Columbian Wari culture between 100 and 600 AD in what is now the Miraflores neighbourhood.
In 2010, archaeologists found the remains of a woman with four children, and in 2008, the remains of a teenage girl.
The site was built on 2.5 hectares of land and towers over 20m (66ft) high. So far, only about 40% has been excavated.
The Wari culture flourished between AD 500 to 1,000 on the coastal area of northern Peru.
Little is known about them, as they did not appear to leave a written record.
Archaeologists in Peru have found two mummies more than 1,000 years old in a suburb of the capital, Lima.