According to court documents released Tuesday, Hunter's 13-year-old daughter told their foster mom about physical abuse to Jhessye prior to her being reported missing. The child stated that she was told by her mother to lie to police about Jhessye being missing.
The report goes on to say the child told investigators that Hunter allegedly kept Jhessye in her mother's bedroom closet.
Police said Hunter's children who have been in Child Protective Services since soon after Jhessye's disappearance told police Jhessye has bruises on her.
Glendale police said Monday that Hunter was arrested on child-abuse charges "directly related to her daughter, Jhessye."
Police are still searching for the girl but they are doubtful she'll ever reunite with her family.
Maricopa County Dep. Attorney Rachel Mitchell asked a judge Tuesday to hold Hunter on $250,000 bond. Mitchell pointed to Hunter's past conviction in California on corporal punishment of her kids.
"She has recently tested positive for THC, which indicates drug use, marijuana specifically and also she has been made aware that she is the suspect in a homicide," said Mitchell.
That declaration was the first time an official indicated the investigation into the missing little girl was indeed a homicide investigation.
Hunter also addressed the court during her Initial Appearance. She told the judge she was not a flight risk and she declared her innocence.
"I do plead not guilty, of course, ma'am," said Hunter. "I don't plan to flee. I'd just like to be given a chance to prove my innocence ma'am."
At a news conference Monday afternoon, Glendale police said they do not believe it is likely they will find Jhessye alive.
Jhessye was last seen Oct. 11.
CBS 5 confirmed Hunter was booked into 4th Avenue Jail on child abuse charges around 3 p.m. Monday.
There was a large police presence early Monday morning at the apartment complex at 6800 N. 45th Ave., where Hunter lives, including forensics vehicles.
Hunter recently gave birth to another child and has been recovering at the residence. The baby and four other children are in the custody of Child Protective Services.
In an exclusive interview with CBS 5's Donna Rossi, Hunter said she had nothing to do with her daughter's disappearance.
Police had said Hunter was not a suspect nor a person of interest. But Monday they said that changed within the past few days when they received new information.
Stay with KPHO.com and CBS 5 News as this story develops.