Police exhumed the partially decomposed body of a missing 6-year-old boy Thursday in a mountain forest in Murayama, Yamagata Prefecture.
They were directed to the site by the boy's mother, who said she buried him there after he died in June.
The 25-year-old mother, Yumi Kato, was served an arrest warrant later in the day on suspicion of dumping the body.
The Yamagata Prefectural Police also plans to question Kato on the circumstances that led to the death of the boy, whose name was Sho, investigation sources said.
Kato, who had been arrested in mid-September for alleged aggravated abandonment of her son, told investigators earlier that the boy died while she was driving him to her divorced husband in Akita Prefecture.
But she has since confessed that she repeatedly beat the boy because she was "irritated that he was physically inferior to other boys of his age," according to police.
Sho was suffering from congenital kidney failure and depended on medication.
According to investigations, Kato left her mother's home in Akita Prefecture with the boy in early May, following a divorce and a row with her mother.
In late August, Kato's mother found her living in an apartment in Murayama with a man she met through an online dating site, but neighbors had not seen Sho since June, police said. Kato herself later disappeared.
Police launched a search for Kato and the boy at the request of Kato's mother. They found the woman Sept. 18 in Tsuchiura, Ibaraki Prefecture.