Acting on investigative leads, authorities believe Duke Flores' remains were placed in a dumpster at some point, the San Bernardino County Sheriff's Department tweeted Monday.
In addition to detectives, sheriff's volunteers and landfill personnel are also assisting in the search for Duke's body.
The little boy's mother, 29-year-old Jackee Racquel Contreras, and her twin, Jennifer Rachel Contreras, were both arrested on suspicion of murder over the weekend.
Apple Valley police officers discovered the child had been missing after they went to a home last Thursday to perform a welfare check requested by relatives, according to the Sheriff's Department.
Jackee Contreras told police her son had last been seen more than a week earlier, investigators said. She was taken into custody for not reporting Duke missing.
Authorities searched the area, but could not find the boy. The following day, Apple Valley Police Department officials issued a public plea for help finding the missing child, whose last known location was in the area of Cherokee Avenue and Pawnee Road.
At a vigil Friday night, family members told KTLA Duke has autism and had wandered away from home in the past.
His grandmother, Lydia Gutierrez, said she hadn't seen her grandson in 10 days.
Authorities have remained tight-lipped about what evidence they have to indicate the boy was killed.