Former caseworker Damon Adams and his supervisor, Chereece Bell, were indicted for criminally negligent homicide, official misconduct and endangering the welfare of a child for the death in September of Marchella Pierce, Brooklyn District Attorney Charles Hynes said.
Marchella was repeatedly beaten and tied to a bed and weighed just 18 pounds at the end of her life, The New York Times reported.
The girl's grandmother, Loretta Brett, accused of witnessing the abuse, was indicted on manslaughter and other charges. The mother already faces murder charges.
Hynes is convening a special grand jury to investigate whether the Administration for Children's Services carried out reforms promised after another child's death in 2006.
An ACS report in October said its workers missed or ignored indications that Marchella's mother, who had a history of drug use, was incapable of caring for her.
Hynes said Adams posted an entry in the agency's computer records to make it appear that he had made home visits when he had not.