The explosions took place at a military base in the port city of Bata, leaving many missing under the rubble, the ministry said.
It said at least 17 people had been killed and more than 400 injured.
It said health workers and the fire brigade were providing care to victims and transferring those with serious injuries to hospitals.
Equatorial Guinea is one of Africa’s smallest countries, with just over 850,000 residents. Bata is one of the country’s two cities with populations of more than 30,000, the other being the island-based capital Malabo.