Villagers spotted the wounded orangutan in a lake in the East Kutai district of East Kalimantan province on Borneo two weeks ago. It died days later.
Local police chief detective Yuliansyah said police arrested four members of a family, including a 13-year-old boy, and a neighbour last week.
He said the suspects admitted they shot, stabbed and clubbed the great ape, which they considered a pest because it ruined the family's pineapple plantation.
Yuliansyah, who goes by a single name, said the boy will continue to attend school while the case is underway.