Investigating judge Yaya Karembe ordered his arrest and charged him at a hearing in the capital Bamako, the source said, just hours after several dozen Malian soldiers forcibly entered Sanogo's residence in the city centre to arrest him.
Sanogo was also charged with kidnapping, said the source, adding that "no one is above the law". "Other people" close to Sanogo would be questioned shortly, he said.
Sanogo was ordered in October to answer questions about deaths that occurred during a mutiny against him at his former headquarters in the central town of Kati, near Bamako.
Sanogo was controversially promoted from captain to lieutenant-general in August, prompting fellow ex-junta members also seeking promotion to mutiny at his Kati barracks, and forcing the army to intervene.
The bodies of three missing soldiers were subsequently discovered in and around the barracks and around 20 officers, including Sanogo's former deputy, were arrested.
Sanogo led a group of mid-level officers to overthrow then-president Amadou Toumani Toure on March 22 last year, upending what had been considered one of west Africa's flagship democracies.