Sadiba Koulibaly was sentenced by a military court to five years on June 14 for desertion and weapons offences in a trial his supporters denounced as trumped-up.
He was second-in-command to junta leader Mamady Doumbouya during the 2021 coup that brought them to power.
Prosecutors at a military tribunal said in a statement that he died on June 24.
An autopsy ordered by the prosecutors found his death "could be attributable to severe psychological trauma and prolonged stress" causing a heart attack, the statement added.
Koulibaly's lawyer Mory Doumbouya told AFP however he believed the death was due to "anything but natural causes".
He said his client was "healthy and calm" and had not complained of any health problems since his arrest on June 4.
He said Koulibaly was held in a secret location and the authorities "refused" to let his defence team contact him.
Domestic turmoil has gripped the West African nation since the coup, with the opposition calling for a return to civilian rule.
Under international pressure, the junta had agreed to organise elections by the end of 2024.
But army-appointed Prime Minister Amadou Oury Bah backtracked on that timetable, saying that the military should remain in power until 2025 at least.
After the September 2021 putsch, Koulibaly was appointed as the Guinean army's chief of staff, a post he held until May 2023.
He then became charge d'affaires at the West African nation's embassy in Cuba.
He returned to Guinea in May, saying he had come to demand that the authorities pay the embassy staff's salaries.
He was arrested on accusations of abandoning his post and prosecutors said weapons were found at his home.
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