More weapons have been recovered at an Iranian-backed Shia-backed militant base.
The cause of the crash is not known, which is the third such incident in a month in the Shia-owned armory.
Some think the United States and Israel are responsible for the incident.
Heavy smoke engulfed a part of Baghdad, but this time it was at a military base under the control of a Shiite group that had helped to defeat IS.
Last week, a similar explosion occurred at a military base in Baghdad, sparking a wave of disarray invading parts of the city.
At the time, the bombing was blamed for extreme heat and inadequate storage of weapons.
The government has ordered all deportation of weapons to other parts of the country from Baghdad.
But the explosion in some Iranian-backed camps has prompted speculation that the United States and Israel are involved - in response to Iran's earlier warning that it would use other means to block the fighting. Iran's class is in the region.
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