No one was reported to have died in the incident, military official Mohammad Hasan told reporters at the scene, saying the fire had broken out in a part of the facility that was used to store expired ammunition.
"We've checked the location, perimeters, there are no fatalities," Hasan told a press conference near the site in Bekasi, on the outskirts of Jakarta.
"The expired ammunitions contain chemicals that can be unstable ... There could have been some frictions that sparked the fire," he said.
Footage broadcast by local network KompasTV showed orange flames and billowing clouds of smoke rising into the night sky while loud explosions could be heard from several kilometres away.
Teams of firefighters and paramedics could be seen near the site but could not approach as the fire raged on, according to local media reports.
They said the blaze had started at 6.30pm.
Local resident Arga Nanda told KompasTV he had heard a loud explosion that shook doors and windows.
People ran out into the streets thinking it was an earthquake, he said.
Army official Kristomei Sianturi told the channel authorities were relocating people from nearby neighbourhoods.
Firefighters could not yet extinguish the blaze, he said, adding its cause was unknown.
He also warned residents not to touch any objects that may be been "thrown" outwards by explosions.
