The Taos County sheriff identified the women facing charges as Jany Leveille, 35, Hujrah Wahhaj, 38, and Subhannah Wahhaj, 35.
National Center for Exploited or Missing Children Abdul-Ghani Wahhaj is the four-year-old toddler who went missing last November and was tied to the New Mexico compound that was recently raided.
Medical examiners still must confirm whether the body found at the property in a second search Monday is that of Abdul-ghani Wahhaj, who was three years old in December when police say his father took him from his mother in Jonesboro, Georgia.
The search warrant executed Friday followed a two-month investigation with Clayton County, Georgia, investigators and the FBI into the whereabouts of Wahhaj's son, Hogrefe said.
"We discovered the remains yesterday on Abdul's fourth birthday", Hogrefe said, according to the Associated Press.
"The children are in our custody, and our No. 1 priority right now is their health and safety", New Mexico Children, Youth and Families Department Secretary Monique Jacobson said in a statement. Lucas Morten was jailed on suspicion of harboring a fugitive, Sheriff Jerry Hogrefe said.
Authorities raided the isolated property near the Colorado border last week. Authorities in New Mexico on Tuesday said they have found the remains of a young boy.
He said Federal Bureau of Investigation agents conducted surveillance of the area a few weeks ago but did not find probable cause to search the property.
Georgia authorities said Wahhaj was traveling through Chilton County on December 13 with seven children and another adult when their vehicle overturned.
So far, all five adults have been charged with 11 counts of child abuse, according to the sheriff.
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"The child was found on the inner portion of the compound", Sheriff Hogrefe said.
It came, apparently, from someone inside a makeshift compound hidden in Taos County, New Mexico and made its way to the sheriff's office through someone else who received it and got it to law enforcement in Georgia. Both Wahhaj and Morten were taken into custody.
What authorities found was what Hogrefe called "the saddest living conditions and poverty" he has seen in 30 years on the job.
But a juvenile court judge eventually issued an arrest warrant to question Wahhaj after he failed to let the mother know where Abdul was.
It's unclear whether Wahhaj did in fact do anything to his son, though authorities confirmed that they had reason to believe Abdul-Ghani had been at the compound in recent weeks.
"We are starving and need food and water", read the message.
The FBI and authorities in Georgia indicated to the sheriff's office that there could be weapons on the compound, and deputies learned that there had been a shooting range installed there, Hogrefe said. Three women who are believed to be the children's mothers were detained and released.
The next day, a dozen officers kicked off the "all day" operation, discovering hidden beneath New Mexico's scrubland the two men with an AR-15 rifle, five loaded 30-round magazines and four loaded pistols, including one in Wahhaj's pocket. Wahhaj's relatives, including his -father, an imam at a mosque in Brooklyn, New York, launched a social media campaign to try to find the missing boy.
The Taos County Sheriff said the 3-year-old boy was not among the children which he described as being in heartbreaking condition, starving with no food or fresh water.
Individuals found in the compound, described as a buried trailer, had "no shoes, personal hygiene, and basically dirty rags for clothing", Hogrefe said.