Anthony Bennett, 20, was charged in a federal criminal complaint in Bay City, where he was expected to appear in court. He is not charged in the death of Carnel Chamberlain, but the complaint details the reported physical abuse of the child.
Bennett reportedly had consulted with an attorney after Carnel was reported missing, but no lawyer is on record in the case.
Carnel was reported missing on June 21 while in the care of Bennett on the Saginaw Chippewa Indian Tribe reservation, near Mount Pleasant. Carnel's mother was at work.
For days, investigators searched woods, ponds and the tribe's wastewater treatment areas to no avail. Carnel's body was discovered on Thursday under a wood porch or deck at his single-story home, said Kevin Chamberlain, who is a cousin of Carnel's mother, Jaimee Chamberlain.
According to the criminal complaint, Carnel's mother told investigators that in late May or early June, she saw her son with a bruised and swollen face as well as a cut lip. She told authorities that her son said he was struck by Bennett.
A few days later, according to the complaint, she told authorities she saw Bennett pick up her son by the neck and drop him before dragging him into a room by his foot.
Friday's charge against Bennett is assault resulting in substantial bodily harm.
"Nothing this monumentally horrific has ever happened in our community," said the spokesman, who grew up on the reservation and served as tribal chief from 1997 to 1999.
"Right now, it's a very somber place with a lot of broken hearts," he told The Associated Press on Friday.
He said he didn't know why investigators went back to the house, which had been sealed off by tribal police days earlier.
On Friday morning, a tribal police car sat outside the family's house, less than a mile from tribal police headquarters and the offices of the Saginaw Chippewa tribe. Just beyond the offices is the gleaming Soaring Eagle Casino and Resort, which attracts gamblers from around the state and is the tribe's financial lifeblood.
Judy Klein, 68, of Mount Pleasant, drove to the boy's home about 70 miles north of Lansing on Friday morning to leave some hydrangeas she had grown in her garden.
She said she was "sick about it" when she learned of the child's death.
"I'm a mother. I lost a child," she said, trying to hold back tears. "She was 26 and died in her sleep. I know the grief."
The tribe offered thanks Friday for those who searched for Carnel as well as condolences to his family.
At a vigil for Carnel on Thursday night near Mount Pleasant, which was attended by Jaimee Chamberlain and other relatives, participants sang, played drums and spoke urging love and healing in the face of tragedy.
Carnel "didn't have time to grow up and enjoy life," tribal chief Dennis Kequom told the gathering. "He'll always be with us in our hearts." --
Associated Press writer David Runk in Detroit contributed to this report.