Menifee police Chief John Hill said at a news conference that a human body that matched the description of Terry Dewayne Smith Jr. was found partially exposed in a shallow grave on the family property.
The body has not yet been positively identified.
Hill said the death was the result of a domestic issue at the house.
Terry has a 16-year-old half brother who authorities have said was the last person to see the boy. However, Hill identified the suspect only as a "family member."
Terry had been missing from his Menifee home since Saturday, and hundreds of volunteers have helped search for him.
Riverside County sheriff's Deputy Albert Martinez said investigators dug up remains after serving a search warrant before dawn at the boy's home. There were no details on the condition of the remains.
Volunteers were told to stop searching Tuesday night, because searchers were getting stranded in the desert and causing problems, hours after local officials pledged to continue searching for the boy.
The boy was reported missing on Sunday morning in the Riverside County community about 70 miles southeast of Los Angeles.
Terry was last seen Saturday night, reportedly following his half brother, who told the boy to go home, the Desert Sun said. The boy's mother, Shawna Smith, said she didn't realize he was missing until the next day.
Searches of the area with a bloodhound, horses and a helicopter were unsuccessful. Hundreds of volunteers also joined the effort but days of covering miles of desert in 100-degree temperatures turned up nothing.
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