Police arrested truck driver Yukihiro Saito for allegedly denying food to his son Riku, who is believed to have starved to death in late 2006 or early 2007, the reports said.
The remains were found in an apartment room filled with garbage in Atsugi, Kanagawa Prefecture, southwest of Tokyo on Friday, they said.
The discovery was made after the local child welfare centre reported to the police in May that Riku was not attending a school he was supposed to be enrolled at, they said.
He then started to neglect the boy. He found the child dead when he returned home one day and fled "because I was scared", he was quoted as telling police.
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He kept paying the rent for the apartment while moving to another place himself, the reports said.
The remains had been left in the apartment for more than seven years with no one consulting the police until May.
Riku did not show up at enrolment for an elementary school in 2008 either but welfare officials did not report it to the police.