Iskandar Sitompul also said the blast near the capital Jakarta was believed to have followed an electrical short-circuit in the building.
The explosion blew apart the warehouse belonging to an elite naval combat force, spraying victims with shrapnel and pieces of wood and glass.
"Most of them were injured by pieces of wood and glass that pierced them on their cheek, chest and stomach," Sitompul said.
The depot is among naval facilities located on a small island a short distance from Jakarta's shoreline.