The blasts occurred at a defence ministry ammunitions depot in the southern Jambyl region on Thursday, leaving dozens injured and forcing the evacuation of more than 1,000 people from nearby villages.
All the victims were soldiers and firefighters.
"President Kassym-Jomart Tokayev, having considered a report by defence minister Nurlan Yermekbayev with a request for resignation, accepted it," presidential spokesman Berik Uali said on Facebook.
In another post later on Tuesday, Uali said the president had appointed Murat Bektanov as the country's new defence minister.
After the blasts, Tokayev had acknowledged that the ex-Soviet country had "systemic problems" with its ammunitions storage and called for authorities to investigate the incident.
Regular incidents at Kazakhstan's Soviet-era military depots have proven a headache for the government.
Another depot near the southern town of Arys has seen three lethal explosions in the last decade.
Sunday was a day of national mourning for the military personnel and rescuers who died at the scene of the disaster.
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