The father of a missing three-year-old who was arrested at a New Mexico compound linked to “extremist Muslims” last week was training children to commit school shootings, court documents filed on Wednesday revealed.

Prosecutors allege Siraj Ibn Wahhaj, 39 (shown above), was conducting weapons training on the compound, where 11 children were found hungry and living in squalor.

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They asked that Wahhaj, who appeared in court on Wednesday, be held without bail.

Wahhaj is the son of a Brooklyn imam, also named Siraj Wahhaj, who was named by prosecutors as an unindicted co-conspirator in the 1993 World Trade Center bombing, the New York Post reported.

Authorities raided the compound on Friday after a months-long search investigating the disappearance of Abdul-Ghani Wahhaj, a boy with severe medical issues who went missing from Georgia in December.

On Monday, a child’s remains were found on the property, but authorities were working on a positive identification and did not confirm if the remains were that of the missing boy.

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Lucas Morton; Jany Leveille, 35; Hujrah Wahhaj, 38; and Subhannah Wahhaj, 35, were also arrested on the property on Friday, and all face child abuse charges.

The makeshift compound — located near the Colorado border — was found shielded by old tires, wooden pallets and other debris.

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Upon authorities’ arrival, Wahhaj was “heavily armed with an AR-15 rifle, five loaded 30-round magazines, and four loaded pistols, including one in his pocket when he was taken down,” Taos County Sheriff Jerry Hogrefe said.

The sheriff said the children, ages one to 15, “looked like third-world country refugees not only with no food or fresh water, but with no shoes [or] personal hygiene and basically dirty rags for clothing.”

The only food investigators found were some potatoes and a box of rice inside a dirty trailer, the sheriff said, adding that the living conditions were “the ugliest-looking, filthiest,” he’s ever seen.

Hogrefe previously said the occupants of the compound were “most likely heavily armed and considered extremist of the Muslim belief.”

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In a warrant made public on Monday, Wahhaj told the missing boy’s mother that he wanted to perform an “exorcism” on his then-three-year-old son because he was “possessed by the devil.” The missing child reportedly suffered from seizures and couldn’t walk.

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Wahhaj’s family background was already controversial prior to his arrest.

In addition to his father’s reportedly being named by prosecutors as an unindicted co-conspirator in the 1993 bombing, the elder Wahhaj, who heads Masjid At-Taqwa mosque, was a character witness in the trial for Sheikh Omar Abdel-Rahman, the notorious “blind sheikh” who was convicted in 1995 of plotting terror attacks in the U.S.

Fox News’ Katherine Lam and the Associated Press contributed to this Fox News piece, which is used by permission.

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