President Bongo, 59, has been out of the country since October seeking medical treatment – first in Saudi Arabia, followed by Morocco. AFP says he is now recovering in a private residence in the capital, Rabat.
Until now, there had been no official confirmation of the nature of Mr Bongo’s illness, just that he had been “seriously ill”.
“Nobody should rejoice over the death or illness of another”, AFP quotes Gabon’s Vice-President Pierre Claver Maganga Moussavou as saying in a speech on Saturday.
“Those who have never known a CVA [meaning cerebrovascular accident or stroke], pray to God that they never know one.”
Ali Bongo succeeded his father Omar Bongo as president in 2009, who governed the oil-rich nation for more than 40 years.
The Bongo family has governed the oil-rich equatorial African nation for five decades and long maintained close ties with former colonial master France.
Diplomatic ties cooled after Ali Bongo was elected in 2009 following his father’s death and French authorities launched a corruption investigation into the family’s assets.