The 68-year-old man told police he dumped his wife's ashes into the toilet bowl at a Tokyo supermarket immediately after she was cremated last month.
Police were alerted after the ashes, and bone fragments including a human chin, were discovered, but were at a loss to explain them until the man handed himself in, the Yomiuri Shimbun reported.
He had felt growing resentment towards his spouse over the years of their unhappy marriage, according to the daily.
His wife had died at the age of 64, following an illness.
Prosecutors are now considering whether to lay charges of abandoning a human body, as ashes can only be scattered in approved locations, a Tokyo police spokesman told AFP.