The first explosion was heard at around 6:00 pm (1100 GMT) on Saturday at a depot used to store expired ammo inside a military complex near Jakarta, TRT reports.
Twenty-seven fire trucks were deployed to the location and firefighters managed to douse the blaze by 3:45 am Sunday.
"We can confirm the fire has been put out, but we are still conducting the cooling down process at the moment to anticipate the possibility of other fire spots," Jakarta city military chief Mohamad Hasan said during a televised press conference.
"Praise God, there have been no fatalities until now," he said.
Authorities had evacuated nearby residents to safer areas as the fire tore through the storage facility but most people have since returned home, according to Hasan.
He said the military had received reports that shells or other projectiles may have landed in the surrounding areas and urged people not to touch the objects, adding that the military was scouring for potentially hazardous materials.
According to the military commander, the warehouse had no electricity and the explosion might have been caused by unstable expired ammunition.
"We suspect this (the explosion) was caused by expired ammunition," he said.
"It is possible that the chemical and explosive material was unstable."
MNA/PR