Ivo Garrido said that at least 300 people were injured and that the toll was expected to increase.
Garrido said the casualties included military personnel working on the site and civilians living in nearby houses.
The cause of the blast, which occurred late Thursday afternoon, was still unknown. One possibility was the searing heat which was blamed for a smaller explosion in January, when three people were injured.
Several thousand people spent the night on the streets in downtown Maputo, unable to return to their homes in the poor neighborhood near the ammunitions depot, which was sealed off by police.
A few people tried to return to their homes Friday as the fire was brought under control.
President Armando Guebuza canceled a one day visit to South Africa for talks with President Thabo Mbeki. He appeared on television late Thursday to appeal for calm.
The area was sealed off by police as scenes of panic unfolded in the capital. Downtown streets were filled with people fleeing the area, with hundreds preparing to sleep outside because they were unable to return to their homes and others desperately searching for loved ones.
At the height of the fire, some city center windows were shattered by the intense heat. Buildings also shook with the impact of the explosions.
The national armory is used to store weapons and ammunition, including some from Mozambique's long civil war. It was the scene of an explosion in January, when three people were injured.
Guebuza said the military was working to determine the cause of the blasts.
Mozambique, an impoverished southern African nation still recovering from a long civil war, has been battered by natural disasters this year. Aid agencies have credited Mozambique's good emergency response system with limiting the casualties.
Heavy rains have inundated much of the country since January, causing flooding and prompting tens of thousands of people to be evacuated from their homes. A cyclone hit coastal resorts last month, killing 12 people and battering the nation's fledgling tourist industry. And earlier this week, more homes on the coast were evacuated and sea defenses breached by exceptionally high tides.
The southern part of Mozambique, which includes Maputo, is in the grip of a fierce drought and blistering heat wave. Temperatures in the capital Thursday reached 95 degrees. Authorities blamed the fire at the weapons depot in January on the heat.