The explosions occurred early on Thursday after a fire broke out at the Soviet-era depot near the town of Kagan, home to 50,000 people, in the Bukhara Region.
"According to preliminary information, three people were killed and another 21 injured in the blasts," the ministry said.
The Defense Ministry said that people living in the vicinity had been evacuated and that the fire was contained after a few hours.
A resident of nearby Bukhara, the Central Asian country's fifth largest city, earlier told RIA Novosti that the blasts, sending artillery shells shooting into the air, could be heard from Bukhara, and had been ringing out all through the night. He said Kagan residents were fleeing to Bukhara.
A special commission involving government officials as well as Defense Ministry, General Prosecutor's Office, Interior Ministry and emergencies ministry representatives, has been set up to assist those injured and investigate the cause of the incident.
The Ministry of Emergency Situations denied media reports that the blasts had destroyed the local railway station and a hospital, and that aviation ammunition had been stored at the depot.
The Kagan area was home to a combined helicopter squad involved in the Soviet Union's military missions in Afghanistan. There is a natural gas field near Kagan, and several trunk gas pipelines.
