The children, between the ages of 1 and 15, are now in protective custody.
Police said Wahhaj was heavily armed with an AR15 rifle, five loaded 30 round magazines, and four loaded pistols.
Asked whether the two men and three women arrested at the compound offered any information regarding the whereabouts of the boy, Hogrefe said they provided some "limited" information that assisted in the discovery of the set of remains, which appeared to belong to a small child.
From left: This Aug. 3, 2018, photo released by Taos County Sheriff's Office shows Lucas Morten.|A handout photo made available by Taos County Sheriff's Office shows the booking photo of Siraj Wahhaj issued on Aug. 05 2018.
Authorities are continuing their search for a three-year-old Georgia boy whose father, who allegedly abducted him, was arrested Friday in what officials call a "third-world"-like New Mexico compound". But surveillance of the property didn't identify Wahhaj or his son there, the sheriff said. The group told police they were headed to New Mexico to go camping, and continued on their way.
No one was injured during the raid, which began Friday morning and lasted all day, the sheriff's office said.
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CBS affiliate KRQE-TV reports that the malnourished children are in the custody of the state's Children, Youth and Families Department. Five adults who were living there face child abuse charges.
The father of a missing Georgia boy is expected to make his first court appearance Tuesday, which could shed light on a freakish tale of guns, exorcism and child abuse at a New Mexico compound.
"We all gave the kids our water and what snacks we had - it was the saddest living conditions and poverty I have seen", Hogrefe said.
The Sheriff said the Federal Bureau of Investigation had "recently provided information and surveillance on this location, but they (FBI) didn't feel there was enough probable cause to get on the property".
The three women at the compound were arrested without incident. The child was found on the "inner portion of the compound", and the sheriff said that information law enforcement agencies obtained led them to a "good idea of a target location" of where to look for the child.
"That all changed for me when a message was forwarded to us from a Georgia detective that we reasonably believed came from someone at the compound".
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It was not immediately known on Monday whether Mr Wahhaj and the others charged in the child abuse case in New Mexico - another man and three women believed to be the mother of the 11 children - had retained attorneys.
While a warrant was issued, criminal charges were not filed against his dad, Siraj Wahhaj, as authorities say there was no custody issue and they simply wanted to know where the child was.
Hogrefe said that Federal Bureau of Investigation agents had surveilled the compound a few weeks previous but did not at the time find probable cause to conduct a search.
Sheriff Jerry Hogrefe says two men were arrested during the search - one on a Georgia child abduction warrant and the other on suspicion of harboring a fugitive.
The Badgers told CNN they found what looked like a shooting range, with tires stacked up to stop the bullets, bullet holes and casings at the compound. "He needs everything. I don't know if he's alive, or he is, well, I don't know his condition now".
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