The girl remains in critical condition at University of New Mexico Children's Hospital in Albuquerque where she is in a coma because of head trauma, police said.
The hospital is not releasing any information about the girl's condition, spokesman Luke Frank said.
Daniel Nicholas Garcia, 32, was arrested Monday for child abuse resulting in great bodily harm, which is a first-degree felony, and a third-degree felony for locking the child in her bedroom, San Juan County Sheriff's Office Det. Tim Nyce said.
Garcia is in custody at San Juan County Adult Detention Center on a $500,000, cash-only bond.
The state has taken custody of the victim and her siblings, Nyce said.
The 5-year-old girl received medical treatment twice in recent weeks for injuries.
On July 25, the girl was taken to an urgent care facility because of a laceration on her chin and a bump on her head, according to court documents.
On Aug. 13, detectives started investigating the girl's family when she was taken to San Juan Regional Medical Center because she was having seizures caused by head trauma, according to court documents.
A doctor at UNM told detectives Aug. 15 the girl was a "horribly beaten child," according to court documents. Doctors said the girl's head appears to have been slammed against the floor and her brain was
The doctor "stated that (the girl) is not breathing on her own and may not live," Nyce wrote in the police report. "She told me (the girl) had been through a lot of trauma."
The girl had been living with Garcia since January. Garcia and the girl's biological mother, Joanna Lewis, were embroiled in a custody battle and the mother hadn't seen her daughter since February, Nyce said.
The girl and her half brother and two half sisters, who lived with Garcia and his wife in a trailer near Bloomfield, were removed from the home and placed in the custody of the state of New Mexico Children Youth and Families Department because of the abuse allegations, Nyce said.
CYFD can take custody of children for 48 hours because of a family crisis and a judge must rule if the agency can continue custody for 10 days, said Enrique Knell, a spokesman for the department.
The agency must go before a judge frequently to continue to keep custody, Knell said.
CYFD makes medical decisions for children within its custody but may consult with the parents, Knell said.
Police believe the girl suffered the serious head injury on Aug. 13, Nyce said.
That afternoon the girl and her 3-year-old brother were told by their parents to take trash outside and the children spilled the trash. The attack may have been prompted when the girl walked away from her stepmother who was telling the victim to wash her hands and clean up her toys.
"I always have to tell (the 5-year-old girl) not to walk away while someone is talking to her and that she needs to listen to people," Garcia told police during an interview, according to court documents.
During the interview, Garcia admitted to police he pushed the girl, according to court documents.
Garcia also told police during the interview the girl may have injured herself by accidentally falling, according to court documents.
Garcia was charged with the first-degree felony because of the serious abuse the girl suffered, Nyce said. He was charged with the third-degree felony because of the small room where he kept the girl locked.
The room had nothing in it but a bed with no sheets, trash bags full of the girl's clothes and a small toilet used to teach toddlers to use the bathroom, according to court documents.
There was a deadbolt lock on the outside of the door to keep the child in the room.
"I did not see any toys in the room, no Barbie dolls or dolls of any kind like you would see in a little girl's room," Nyce wrote in the police report. "I remembered thinking, I wonder if (the girl) gets cold at night."