Soldiers in the West African country say they launched a coup “to restore democracy”.
They took control of the national radio station at 04:30am local time to read a short statement announcing a “National Restoration Council”.
Tanks and armed vehicles can be seen on the streets of the capital Libreville.
Ali Bongo succeeded his father Omar Bongo as president in 2009. He narrowly won re-election in 2016 in a poll marred by violence and accusations of fraud.
Bongo, who has been out of the country for two months, reportedly suffered a stroke in October and received treatment in Morocco.