Two men charged over the abuse of 11 children found malnourished at a ramshackle compound in New Mexico were training them with firearms to commit school shootings, prosecutors say in court documents.

One of the suspects, identified as Huraj Wahhaj, is the father of a young boy whose disappearance from his home near Atlanta months ago prompted the investigation that led authorities to raid the compound, located north of Taos, New Mexico, last week.

Remains believed to be that of the boy, who was three years old when his mother reported him missing, were found at the property on Monday but have not yet been positively identified, authorities said.

Wahhaj, a second man accused of harbouring him as a fugitive, Lucas Morton, and three women presumed to be the mothers of the 11 children taken into protective custody, were each charged with 11 counts of child abuse.

The five defendants made their initial court appearance before a local magistrate on Wednesday. They were due to be arraigned Thursday (AEST).

Taos County Sheriff Jerry Hogrefe told reporters that investigators found a shooting range built at one end of the squalid compound, located on the outskirts of the community of Amalia in northern New Mexico, near the Colorado border.

Wahhaj, 39, whose first name is alternately presented in some court documents as Siraj and is the person described as being “in control” of the compound, was heavily armed when taken into custody, the sheriff said.

A foster parent of one of the 11 children told authorities that Wahhaj “had trained the child in the use of an assault rifle in preparation for future school shootings”, prosecutors alleged in an expedited motion for pretrial detention.

The document further stated that Wahhaj was “under investigation for the death” of a 12th child at the compound, as well as for “training of children with weapons in furtherance of a conspiracy to commit school shootings”.

The court filing also states he “transported children across state lines for the purpose of children receiving advanced weapons training to commit future acts of violence”. 

Similar allegations were levelled in a motion prosecutors filed seeking expedited pretrial detention of Morton.

No mention was made of ideology or motive in initial court filings. The sheriff in comments over the weekend referred to the suspects as “extremists of Muslim belief” but he declined to elaborate on that characterisation when asked about it by reporters at a news conference on Tuesday.

According to CNN, Wahhaj is himself the son of a prominent Muslim cleric in New York.

-AP