The total cost of the damage was about two billion leks ($26m).
Ina Rama, the prosecutor-general, said that the laws and procedures of security and ammunition storage had been violated by Mediu's "actions and non-actions".
She continued that the mismanagement of the disposal process had "caused the spark of the fire followed by the massive explosions".
'Child workers'
She said that children had also been employed in the factory - a "flagrant violation" of the law.
The prosecutor also said that the favouring of a US-Albanian company for the dismantling contract by the ex-minister meant the firm received "unfair profit".
Mediu is the leader of the Republican party, part of the ruling coalition.
He responded at a news conference saying that, although he would co-operate with the investigation, it was one-sided and that he was innocent.
The contract was given to Southern Ammunition company in South Carolina and Albanian Albademil company to dismantle about 18,000 tons of small- and large-calibre ammunition, for $583,000.
A defence ministry official, the owner and the manager of the Albanian firm have been arrested for violating explosives laws. Two additional senior officials have been charged.