Military officers say they have seized power in oil-rich Gabon, where the ailing leader’s family has ruled for 50 years.
The soldiers took control of the national radio station at 04:30 local time (03:30 GMT) to read a short statement announcing a “National Restoration Council”.
Tanks and armed vehicles can be seen on the streets of the capital Libreville.
Mr Bongo, who has been out of the country for two months, reportedly suffered a stroke in October and received treatment in Morocco.
The president for the first time delivered his address from the Moroccan capital, Rabat, where he is recuperating from a stroke. He was transferred to Rabat from a Saudi hospital late last year.
Security and political watchers are pointing to the military’s move as an apparent coup attempt. The full extent of the involvement of the military top brass is not yet known.
Mr. Bongo 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.”
“It reinforced doubts about his ability to assume the responsibilities of his role as President of the Republic”, said Lt Kelly Ondo Obiang, the leader of the so-called Patriotic Movement of the Defence and Security Forces of Gabon.
He specifically appealed to young people to “take charge of their destiny”.
The insurgents called on soldiers to take control of the transport system, ammunition reserves and airports “in the interests of the nation”.
There is no word so far from the government.