The bodies of a nine- and 10-year-old girl were found at a home in Albertinia near Mossel Bay on Thursday night.
Police spokesperson Captain Malcolm Pojie says the gruesome discovery was made at around 18:30 after the two girls were reported missing earlier in the afternoon.
Pojie says the body of one victim was found under a bed and the other body was found in a blue plastic drum.
The victims were discovered inside the house of a 53-year-old man who is known to the victims.
Captain Pojie says the man is currently missing and they suspect that he is hitchhiking in the direction of Cape Town.
It is suspected that the girls died as a result of suffocation, but a post-mortem will be conducted on the bodies in George on Friday to determine the exact cause of death.
The children have since been identified as 9-year-old Jacorine Vaaltyn and 10-year-old Sharon Arries.
The incident is being investigated by the Mossel Bay Family Violence Child Protection and Sexual Offences unit.