The boy was reported missing earlier that evening by his mother after he failed to return with his sister from a visit to their father, according to a report in the daily Tagesspiegel.
The eight-year-old girl told their mother that the boy and their father had had a row, prompting the woman to call the police, fearing for the safety of her son.
Officers who called around to the father's house in the Reinickendorf area of the city found traces of blood which led from the cellar door to a wooden partition, behind which they discovered the body of the boy.
A post-mortem conducted the following day ruled out any sexual abuse and concluded the boy had been killed by blunt blows to his upper body. Investigators say they suspect an argument between the boy and his father which ended fatally.
Police would not comment on reports that the father had separated from the children's mother a long time ago. One officer told the Tagesspiegel that the father had a serious alcohol problem.
Officers initially arrested the flatmate of the father but have since released him and are concentrating on trying to trace the father himself, who has gone missing.