Soldiers in the west African country say they launched a coup "to restore democracy".
They took control of the national radio station at 04:00 local time (03:00 GMT) to read a short statement announcing a "National Restoration Council".
President Ali Bongo took over power in 2009 and has been out of the country for more than two months, reports BBC.
Tanks and armed vehicles can be seen on the streets of the capital Libreville. President Bongo reportedly suffered a stroke in October and received treatment in Morocco.
He sought to put an end to the rumours about his health with a televised New Year message in which he said he was feeling fine. Soldiers said they had been disappointed by the message, calling it "a pitiful sight" and a "relentless attempt to cling onto power."
The insurgents called on soldiers to take control of the transport system, ammunition reserves and airports "for the good of the country"reports Radio France Internationale.