The former army general had won acclaim for pursuing democratic reforms before being toppled by a military coup in 2012.
Authorities in Mali say they have opened an inquiry into the violation of state security, a move that came after half a dozen prominent figures were detained for questioning earlier this month.
The country, which underwent a coup in August, is in the hands of a transitional government scheduled to oversee a return to civilian rule within 18 months.
The public prosecutor in the capital Bamako said a “preliminary inquiry” had been launched by judicial investigators “following a report by the security services relating to violations of state security”.
“The accused … have been placed at the disposal of the [investigators],” prosecutor Mamoudou Kassogue said in a statement, adding that the inquiry was “ongoing”.
Six people were detained on December 21, including Aguibou Tall, who is the half-brother of former Prime Minister Boubou Cisse, and the secretary of the president’s office, Sekou Traore, according to security sources.
Another well-known figure is campaigner and radio presenter Mohamed Youssouf Bathily, who is popular among young Malians.
In the run-up to their arrest, social media said there had been a scheme to “destabilise” transitional institutions set up after the August 18 coup.
Cisse, the last prime minister under former President Ibrahim Boubacar Keita, denied any involvement in such schemes.
His home in Bamako was searched by unidentified men on December 24, his lawyers said.
The Malian Association for Human Rights (AMDH) said it had visited those detained at a gendarmerie base between December 24 and 27.
Bathily’s lawyer, Zana Kone, said his client was well and had not been maltreated, although his dreadlock-style hair had been shaved off.