The grim discovery was made in the case that has spanned three California counties after authorities first found a severely abused 9-year-old girl at an apartment in Plumas County last week.
Further investigation led police to a missing children's case in Salinas, Monterey County, and eventually to the bodies of a 3-year-old and 6-year-old child in a plastic container at a storage unit in Redding in Shasta County.
The 9-year-old girl was being treated for injuries at a Sacramento area hospital.
"She is in a safe environment," Flippo said.
The dead children were discovered after a welfare inquiry about two children in Huntsman's custody, who police said were reported as missing.
McMillin said that an autopsy performed Wednesday determined the two children likely died from continued physical abuse.
"We are confident that the abuse that ultimately led to their deaths began here in Salinas," he said.
Authorities have not positively identified the dead 3-year-old and 6-year-old as the missing children, but said they are convinced of their identities.