"A navy ammunition depot exploded this morning but we are still checking the details," Jakarta police spokesman Rikwanto told AFP.
Local television quoted the country's military spokesman Iskandar Sitompul as saying 25 people were injured. No further details have been provided.
The depot is located on a small island off Jakarta's coast.
Indonesian media reported a number of ambulances were parked at a Jakarta pier from which the island is reachable by boat.
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