File Photo: Former President of Guinea, Alpha Conde (C) casts his ballot in the ballot box during the presidential elections in Conakry on October 18, 2020. AFP
The 84-year-old Conte, who was ousted last year, has been allowed to travel out of respect for his "dignity and integrity" and for "humanitarian reasons", the junta's governing body said.
Conde has "medical appointments" abroad, the National Rallying Committee for Development said, without providing details about his health, where he would be treated or the length of time he would be out of the country.
However, according to an airport management official and a police official, Conde boarded an aircraft bound for Turkey at Conakry airport in the morning.
They added that the former leader appeared to have left on his own.
Guinea earlier this month opened a judicial investigation into Conde and several other former top officials for murder, torture, kidnappings, looting and rapes.
Army officers led by Colonel Mamady Doumbouya ousted him last September after 11 years in power in the impoverished former French colony.
Conde had drawn fierce criticism after he pushed through a new constitution in 2020 that allowed him to run for a third presidential term.
He was initially detained before being allowed to go to the United Arab Emirates for medical treatment in January, returning home in early April.
On April 22, the junta declared Conde was "finally free", but he has not been seen in public since.