Judicial sources in Bamako on Sunday, speaking on condition of anonymity, had said charges had been filed against the group, but negotiations between Ivory Coast and Mali were continuing.
In a statement, public prosecutor Samba Sissoko said the 49 had been ordered to be held in custody after being charged on August 10, 11 and 12.
The charges comprise "criminal association, attacking and plotting against the government, harming state external security, holding, carrying and transporting combat weapons and complicity in these crimes," Sissoko said.
The soldiers were arrested after their arrival at Bamako airport on July 10.
Ivory Coast says they were sent on a routine rotation for personnel who provide backup services for the UN peacekeeping mission in Mali, MINUSMA, and has called for their release.
Mali's military-led government says the troops had had no orders or supporting documents and has described them as "mercenaries".
Negotiations are underway to free the soldiers, with Togolese President Faure Gnassingbe acting as a mediator, but a first round of talks, held in the Togolese capital Lome on July 28, failed to make progress.
The current president of the African Union (AU), Senegalese President Macky Sall, is expected to bring up the issue at a meeting in Bamako on Monday with junta leader Colonel Assimi Goita.
Others who have intervened are the head of the High Islamic Council of Mali, Cherif Madani Haidara; the archbishop of Bamako, Jean Zerbo; and Cherif Bouye Haidara, an influential religious leader in the southwestern town of Nioro.
A source close to the Ivorian army said Ivory Coast would await the outcome of the mediation efforts before responding.
The Malian junta has previously accused Ivory Coast of encouraging the West African regional bloc ECOWAS to toughen its sanctions against the regime following a coup in August 2020.
The sanctions -- imposed over perceived foot-dragging by the junta over the timetable to restore civilian rule -- were eventually lifted in early July.
Meanwhile, France says it has withdrawn the last of its troops from Mali, though it says it will remain in the area for further counter-insurgency operations.