Samuel Shaffer faces two counts of kidnapping and four counts of child abuse.
Authorities said Shaffer took the two other girls, one of his daughters and the 8-year-old missing girl, with him to a different location.
Authorities believe the girls may be with Shaffer because they are betrothed to him for marriage.
John Coltharp, the biological father of Hattie and Dinah (the two girls in the original Amber Alert) was charged Tuesday with one count of child kidnapping and obstruction of justice after charging documents say he refused to tell officer where the children were.
The Iron County Sheriff's Office in Utah says it's executing three separate search warrants along with help from the Federal Bureau of Investigation. Along with them, deputies found two other young girls who are the biological daughters of the man suspected of detaining them.
Self-proclaimed cult leader Samuel Shaffer, who was believed to have been given the children by their father, has been taken into custody by the sheriff's department in Iron County, Utah, in connection with the incident.
The brothers, Seth Coltharp, 6 and William Coltharp, 7, were found Monday morning when the Iron County Sheriff's Office raided a compound belonging to a group called the Knights of the Crystal Blade.
Shaffer and the two girls' father, John Coltharp, were said to have been involved in "cult-like activities".
The girls' mother, Micha Coltharp, claims her ex-husband joined Samuel Warren Shaffer, 34 in a religious sect called the "Knights of the Crystal Blade".
The Spectrum reported, Shaffer has been arrested by the Iron County Sheriff's Office. His ex-wife was granted custody on November 27, but the search for them intensified when Coltharp was arrested and refused to reveal their location.
Micha Coltharp had legal custody of the children after a recent divorce.
When deputies responded to the area, they found Shaffer, and he was taken into custody without incident. He is being held on a $50,000 cash bond. Shaffer reportedly stated the girls had been placed in the barrels to conceal or hide them from those searching for them.
"At this time it appears the children had spent approximately 24 hours inside the barrels in subfreezing temperatures. Shaffer also made statements he had left a firearm behind on the ground next to the barrels".
Court documents state those two girls were found "in poor health with signs of dehydration and acting lethargic".
"The youngest child: Samantha Shaffer has since been flown by Life Flight helicopter to Primary Children's Hospital due to her condition". As of this afternoon at 5 p.m., her condition is unknown.
All four young girls went to the hospital; three have since been released.
The investigation is ongoing.