Soldiers in the oil-rich West African country say they launched a coup "to restore democracy", a report by BBC on Monday said.
Gabon will be ruled by "a national council of restoration" which will be set up shortly, Ondo Obiang said.
A crowd of around 300 people have gathered outside the radio station in the capital Libreville, apparently showing their support for the military takeover. No violence has been reported.
The Bongo family has ruled the oil rich country from almost 50 years with his father Omar Bongo Ondimba at the helm for 42 years until 2009 when his son Ali Bongo succeeded him. He recently addressed the country in a New Year's message that was filmed in Morocco, where he has been receiving medical treatment.
In a New Year's day broadcast, he tried to put an end to the rumour about his health, assuring citizens that he was fine.
President Ali Bongo who is now recovering from a stroke in Morocco took over the country's rulership from his father, Omar Bongo, who ruled Gabon for 42 years before his death in 2009.
Stroke-hit Bongo is at present not in the country.
The 59-year-old leader has not been back to Gabon since he fell ill in Saudi Arabia on October 24.
Presidential spokesperson Ike Ngouoni later told AFP, "This speech is proof that President Ali Bongo is fully recovered". He slurred some of his words and did not move his right arm, but otherwise appeared in reasonable health.
Local news described the event as an "attempted coup d'etat" and said the Gabon Republican Guard was seizing power. His re-election in 2016 was marred by claims of fraud and violent protest.