Bongo was "following appropriate treatment" and "taking a few days of rest [before] resuming his activities at the soonest opportunity", a presidential statement said on Thursday.
Sources close to the president in Libreville, Gabon's capital, said that Bongo had had an operation and was "better" following the procedure.
News of Bongo's admission to hospital comes two weeks after he announced that he was temporarily suspending his duties to rest and mourn the death of his wife last month.
Bongo "has been through particularly difficult times with the illness of his wife," an official statement read on national television at the time said.
The announcement came hours after a French judge said that an investigation was under way into the financial activities in France of Bongo, as well as Denis Sassou Nguesso and Teodoro Obiang Nguema, his respective counterparts from Congo-Brazzaville and Equatorial Guinea.
Transparency International France said that the leaders embezzled millions of dollars of public money to fund a lavish lifestyle.
All three leaders have denied the claims.