The Dallas County Medical Examiner's Office concluded the remains found Saturday in Ellis County are those of Johnathan Ramsey, who police allege was starved to death by his parents, The Dallas Morning News reported.
Ellis County Justice of the Peace Bill Woody told the newspaper the medical examiner sent him a report Tuesday that concluded the boy's death was a homicide.
Authorities were directed to the creek by the boy's father, Aaron Ramsey, who told Dallas police he put the body there last year. The remains were discovered "in 3-foot water under a log," Woody said.
He said the medical examiner's office plans to run DNA tests on the bones and do other forensic testing in an attempt to determine how the boy died.
The father and the boy's stepmother, Elizabeth Ramsey, are in jail on charges of injury to a child.
The search for Johnathan began late last month after Aaron Ramsey's father told police he had not heard from his grandson since January 2011.
The newspaper said the couple allegedly confessed to locking the boy in a bedroom for months last year, limiting his nourishment primarily to bread and water. Court documents indicate he became so frail and hungry he ate his own feces.
Aaron Ramsey told investigators he locked the boy in a room after he began behaving violently. He alleged Johnathan punched his stepmother, who was pregnant with triplets, in the stomach, causing her to miscarry.
Authorities suspect the boy died around August.