Rights groups say the colony's leaders helped with the repression of left-wing activists during military rule.
It is thought dozens of bodies were buried at the enclave formerly known as Colonia Dignidad, but later moved.
Last year, the state took control of the enclave. Its former head, Paul Schaefer, is in jail charged with child abuse and human rights violations.
Judge Jorge Zepeda is expected to inspect the unmarked grave on Tuesday.