The Office of the Medical Investigator identified the remains of three-year-old Abdul-Ghani, who was from Jonesboro, Georgia, when he was reported to be missing.
Prior to identifying Abdul-Ghani’s body, the Taos County Sheriff’s Office in New Mexico had raided the compound they referred to as a “makeshift residence” on 3 August and found 11 children ranging in age from one to 15 years old.
Taos County officials said their raid followed a search warrant which came after a two-month investigation following allegations that Abdul-Ghani’s father, Siraj Wahhaj, abducted the child from Georgia.
Police said Mr Wahhaj was among the five adults found at the compound during the raid.
All five adults face 11 counts of child abuse, CNN reported. They have pleaded not guilty.
Authorities claim to have found firearms including an AR-15 on the property.
Owners of the compound, Jason and Tanya Badger, claimed in an interview with CNN that they alerted authorities that they saw the child months prior to the raid.
Taos County Sheriff Jerry Hogrefe said that information was not reported to him at the time. Mr Hogrefe said in a press release that he began working on a search warrant for the property when they received a tip that children on the compound were “starving” and in “need of food and water”.
Abdul-Ghani’s mother had told authorities that her son suffered from seizures, developmental and cognitive delays and Hypoxic Ischemic Encephalopathy, a birth injury caused by lack of oxygen and blood flow to the brain.
"Our thoughts and prayers go to Wahhaj's family,“ said Alex Sanchez, public information officer for The University of New Mexico Health Sciences Centre.
”We certainly understand the heartbreak this news will cause and want to stress our commitment to investigating this death to serve the living."
Prosecutors say the adults were training the children to use firearms and that the boy died during a religious ritual.
“This was not a camping trip and this was not a simple homesteading, the kind that many people do in New Mexico,” said prosecutor Timothy Hasson. “The evidence as a whole suggests that this family was on a mission. And it was a violent one, and it was a dangerous one."
Thomas Clark, Mr Wahhaj's lawyer, said: "If these were white people of a Christian faith who owned guns, that's not a big deal because there's a Second Amendment right to own firearms in this country."
Prosecutors argued that the suspects be held in jail without bail pending trial but a state district judge allowed the release of four of the suspects – not Mr Wahhaj – to house arrest with conditions.
A bond was set at $20,000 (£16,000). According to the Associated Press, Mr Wahhaj will remain in jail pending a Georgia warrant for his arrest for accusations of child abduction.