Ten massive Il-76 cargo planes and five Mi-8 helicopters are water-bombing the area, near the town of Achinsk in the Krasnoyarsk region.
A defence ministry statement said "there are no more fires" at the site, an old dump due for closure housing some 55,000 artillery shells.
More than 9,500 people were evacuated.
Six injured people are in hospital, but they are not critically ill.
Flying munitions damaged a school and a kindergarten in the village of Kamenka. But Deputy Defence Minister Gen Dmitry Bulgakov said that besides smashed windows there was little structural damage in the area.
Local residents were evacuated from inside a 20km (12 miles) radius around the arms dump.
Witnesses posted videos of balls of flame and black smoke, starting during the day and continuing after dark.
Krasnoyarsk region is one of those affected by huge wildfires that engulfed parts of Siberia in recent weeks, due to unusually hot weather and strong winds.
The worst of the fires, however, were many miles away to the north-east.
Military sources told the government newspaper Rossiiskaya Gazeta they believe the explosions were triggered by an old shell blowing up in an army truck.