Colonel Celestin Bilivogui is the second military officer in recent months to be pronounced dead in mysterious circumstances after being arrested under the junta, in power since 2021.
Bilivogui's lawyers said he was taken by security forces from his office in the military pensions department early last November before being moved to an unknown destination.
His wife and lawyers said they had not heard from him since.
The incident took place days after former dictator Moussa Dadis Camara and three others on trial over a 2009 massacre escaped from prison in the capital.
The armed prison break left several dead and raised fears of another coup in the West African country.
Bilivogui was dismissed from the army in the days after along with dozens of military personnel.
On Wednesday, his wife was called to the main military administration centre in Conakry and taken to a morgue "where she was presented with the body of her husband", one of their lawyers, Salifou Beavogui, said in a message passed onto the press.
A family member confirmed the information to an AFP journalist.
"Kidnapped and held for a year, he has had no right to a trial or to justice," Beavogui said.
The authorities have not commented on the issue.
In June, ex-army chief of staff and the junta's former second-in-command, General Sadiba Koulibaly, died in detention days after being sentenced by a military court for desertion and weapons offences.
Two anti-junta activists Oumar Sylla, better known as Fonike Mengue, and Mamadou Billo Bah, have been missing since they were arrested by security forces in July, their pro-democracy movement says.
Guinea's opposition has faced severe repression since junta leader Mamady Doumbouya seized power in a coup in September 2021.
Many opposition leaders in Guinea have been detained, brought before the courts or forced into exile.
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