Conde, who was ousted in a September 2021 coup after more than a decade in power, has been living in exile in Turkey.
He is already being investigated for alleged corruption, assassination, torture, kidnapping and rape.
"You are ordered... to initiate legal proceedings for alleged acts of treason, criminal conspiracy and complicity in the illicit possession of arms and ammunition," Justice Minister Alphonse Charles Wright said in a letter to the public prosecutor of the capital Conakry on Monday.
The letter alleged that Conde had acquired weapons and ammunition, without providing details.
In 2010, Conde became the first democratically elected president of the former French colony after decades of authoritarian and dictatorial regimes.
His decision to run for a third term triggered strong protests, which were violently repressed. After the 2021 coup, Colonel Mamady Doumbouya seized power and has promised to hand the reins of government to elected civilians by January 2026.
The junta has launched a slew of prosecutions against people close to Conde.
Mali, Burkina Faso and Niger have each also undergone at least one coup since 2020.