Elisa Baker has been charged with obstruction of justice after police said she admitted writing a phony ransom note before calling in a missing persons report. Police have said she is cooperating with the probe.
Zahra was reported missing by her stepmother and father on Oct. 9, but police say no one outside of the family has reported seeing her since Sept. 25.
District Attorney James Gaither Jr. did not say if Zahra was dismembered or if more charges were imminent, according to The Associated Press.
The girl had a grueling life. Stricken with bone cancer, she lost her left leg and much of her hearing. Relatives and neighbors said that Elisa Baker, 42, was abusive to Zahra, who was often bruised.
Her prosthetic leg was found recently on Christy Road, in the same rural area that her remains were uncovered.
Last week, investigators discovered a bone that police say "may be related to" the case. Police have sent the bone to a medical examiner's office to determine its relation to the case.
Police have also searched a landfill, the Bakers' home, areas where Elisa Baker formerly lived, and drained two ponds in the hunt for Zahra's remains. They pulled a mattress from the landfill and are testing it for DNA evidence, police have said.
Nov. 16 would have been Zahra's 11th birthday.
Jailhouse letters, apparently written by Elisa Baker, claim police know exactly where the girl's body is located.
The letters maintain neither Elisa Baker nor her husband killed Zahra, but that the father did something "horrifying" after the girl was dead.
The letters, obtained by ABC News, appear to shift any blame from Elisa Baker to her husband Adam Baker.
"We really didn't kill her, but what he did after the fact is kinda horrifying," Elisa Baker wrote to crime memorabilia dealer Eric Gein from jail. "[It] makes me scared of him. So I probably am gonna go ahead and file [for divorce]. I have lost my whole life anyway."
Gein, who runs the website SerialKillersInk.net, told ABC News he contacted Elisa Baker by letter weeks ago under an assumed name. The letters he received in return describe strained life in the Baker home. She allegedly signed one letter, "Dark Love Always, Elisa."
Further down the page between doodles of candles and a spider she writes, "Goth's Rule [sic]" and "Vamps Rule!" The comments are similar to those made on a MySpace page believed to belong to Elisa Baker.
"The cops know where she is and what he has done," she wrote, apparently referring to her husband.
"[Adam Baker] knows what happened to Zahra, and yet I'm the one in here at least for now," she writes.