Detectives received a tip Wednesday alerting them to possible human remains that police later confirmed fit the description of Terry Smith, KTLA-TV, Los Angeles, reported.
"Officers on arrival located a partial grave containing partially exposed human remains," Riverside County Sheriff's Capt. John Hill said.
The remains had yet to be identified, authorities said, but Smith's 16-year-old half-brother has been arrested on suspicion of murder.
After the remains were found, authorities called off the long search for Terry, and interviewed the boy's family.
"As a result of those interviews, a 16-year-old family member was arrested for murder," Hill said.
"This was a domestic issue within the residence," he said.
Terry had been living in Menifee, Calif., with his mother, Shawnee Smith, her partner, a 13-year-old girl and a 16-year-old half-brother, neighbors said.
The half-brother was said to be the last person to see Terry Saturday evening. He told police he was walking to a corner store when he saw Terry following him.
He said told Terry to go home and never saw the boy again, police said.
The store manager told KTLA the 16-year-old half-brother wasn't in the store Saturday.
"He wasn't at the market. We had checked our surveillance, our cameras, all the video ... nothing," the woman said.
Initial reports said Terry Smith was a highly functioning autistic child but his father, Terry Dewayne Smith Sr., who lives in West Virginia, told KCAL-TV, Los Angeles, his son was not autistic.