Marchella Pierce was found dead in her home last month.
Pierce's mother has been charged with assault and child endangerment.
Authorities are looking into whether Administration for Children's Service workers ignored warning signs and went months without visiting the child's home.
Both ACS and the Child Development Service Corporation have been blaming each other.
Pierce weighed just 18 pounds when she died Sept. 2 and appears to have gone months without a visit from the caseworkers who were assigned to check on her, the ACS said in a preliminary report Tuesday in which it admitted mistakes.
The death casts doubt on the effectiveness of reforms that were undertaken after the 2006 death of 7-year-old Nixzmary Brown at the hands of her stepfather.
After Nixzmary's death, the agency hired 540 additional caseworkers and reduced caseloads from 21 to 15.
But the agency Commissioner John Mattingly said at a City Council hearing Tuesday that that the agency was "deeply troubled" by what is known about Marchella's short life.
"Clearly, Marchella Pierce was a vulnerable child, and as a society we needed to do more to help her thrive," he said.
The girl's mother, 30-year-old Carlotta Brett-Pierce, is facing charges that include second-degree assault.
Marchella was born prematurely and spent most of her life in hospitals.
According to an agency report, her mother had a history of drug abuse and seemed incapable of taking care of Marchella.
She told investigators that she had tied Marchella to a bed at night to keep her from taking food out of the refrigerator and making a mess.
The report found that agency workers who were supposed to be monitoring the family made no visits after June.