On Wednesday, prosecutors disclosed the children also had been waterboarded, shot with crossbows and had scalding water poured on them, CBS News reported.
Allen, 29, was served with the arrest warrant Friday and charged with seven counts of torture and nine counts of felony child abuse, according to police.
The bathroom is strewn with feces at a home in Fairfield, Calif., Monday, May 14, 2018, where authorities removed 10 children and charged their father with torture and their mother with neglect after an investigation revealed a lengthy period of severe physical and emotional abuse.
According to Juarez's motion, Fairfield Police came to the family's house in a suburb about 45 miles north of San Francisco on March 31 to investigate one of the children being reported as missing. Once they arrived, they immediately became concerned for the safety and health of the children and chose to search the property-that's when they discovered nine more children, "living in squalor and unsafe conditions".
The children are ages 4 months to 12 years and were removed from his Fairfield home after police found them living in filthy conditions. The children's mother, 30-year-old Ina Rogers, appeared in court Wednesday. She "may not be a danger to the public at large, but these charges make clear she is a danger to the children", he said.
The 10 children shared a single bedroom, Rogers told reporters, while three other rooms served as the master bedroom, playroom and a meditation room. Prosecutors charged Rogers, 31, on Wednesday in Solano Superior Court with nine counts of felony child abuse, saying that she caused the children to be in a situation likely to produce great bodily injury and death.
Fairfield police Lt. Greg Hurlbut on Monday described the home as having human and animal feces and urine on the floor, as well as spoiled food and garbage. She did not say why. She was taken into custody with bail set at $495,000.
He denied the charges and remains in custody and is being held on $5.2m (£3.85m) bail.
In an interview with NBC News, the children's grandmother accused the father of worshipping Satan, claiming that her grandchildren "lived in torture" and that Allen maintained a "devil room" inside the family home.
While police claimed some of the abuse was carried out for a "sadistic" goal, they have declined to reveal what that abuse entailed.
The children did not require medical attention when they were removed, but stories about abuse came out gradually over the past six weeks and eight of the children told professionals about incidents dating back several years, authorities said.
Solano County's Child Welfare Services department officials did not immediately respond Tuesday to request for details about the visit, or information about other interactions they may have had with members of the household. She was released on April 9 after posting a $10,000 bail.
In the motion, Deputy District Attorney Veronica Juarez wrote that the children suffered scars and injuries such as broken arms. Rogers is now caring for several of the children while the others are with relatives, the network reported.
The children had been home-schooled and were seen outside so rarely that some neighbors were shocked to learn more than a few lived at the house. "My husband has a lot of tattoos, he looks like a scary individual, and that's why people are so quick to judge him". Officials took pictures of the children and interviewed them individually, she said.
She now faces nine counts of felony child abuse.
"They were bullied and the teachers weren't helping me with their education", Rogers said.