President Andry Rajoelina left between October 11 and 12 after “explicit and extremely serious threats were made against the life of the Head of State,” the presidency said in a statement late Wednesday.
The threats had come when he was due to travel abroad for a mission, the statement sent to AFP said.
Media reports indicated the 51-year-old leader was evacuated on Sunday aboard a French military plane.
On Monday, he said he had taken refuge in a “safe place” without giving further details.
Rajoelina, who first came to power after a military-backed coup in 2009, accused the National Assembly of colluding with the military to remove him from office.
The military officers who seized power said their leader, Col. Michael Randrianirina, would be sworn in as new president on Friday.
The youth-led Gen Z movement that initiated the protests on September 25 over lack of water and energy welcomed Randrianirina’s intervention.
The international community voiced alarm, with the United Nations censuring what it called an “unconstitutional” takeover and the African Union announcing Wednesday it was suspending Madagascar “with immediate effect.”
Madagascar is the latest of several former French colonies to have fallen under military control since 2020, after coups in Mali, Burkina Faso, Niger, Gabon and Guinea.