The 59-year-old, who fell ill on October 24 at an economic forum, arrived in Morocco last week following treatment in Saudi Arabia for an illness that has not been officially revealed.
The decision to dismiss him from the military hospital in Rabat came “after authorisation from the medical team”, the source in the Moroccan presidency said.
Morocco’s King Mohammed VI had on Monday paid a visit to Bongo at the hospital, with the palace issuing handout pictures of their meeting.
The images failed to put to rest rumours about Bongo’s health, with numerous posts on social media networks back home in Gabon raising doubts about their authenticity.
“The head of state is doing fairly well, the process of his rehabilitation is evolving very quickly and positively,” Prime Minister Emmanuel Issoze Ngondet said in Libreville.
Opposition figure Jean Eyeghe Ndong on Wednesday dismissed Ngondet’s assurances, calling for professional medical bulletins on Bongo’s health.
Bongo arrived in Rabat last Thursday to continue his recuperation and rehabilitation in hospital, after more than a month at a medical facility in the Saudi capital Riyadh.
The Bongo family has governed Gabon for five decades. Ali Bongo was elected head of state after his father’s death.
He was narrowly re-elected in 2016 after beating opposition challenger Jean Ping by a few thousand votes following a presidential poll marred by deadly violence and allegations of fraud.