Bouteflika, who reportedly boarded an Algerian presidential jet in a wheelchair at Le Bourget airport near Paris, was admitted to hospital at the end of April after suffering a mini-stroke.
His plane took off around 1130GMT, the source said.
The health of the Algerian leader has been a source of huge concern in the north African country, where little has been divulged about his condition since he flew to Paris in April.
Last month, Algerian authorities released photos and footage of Bouteflika on state media, showing the 76-year-old in the Paris hospital where he was convalescing.
The pictures were published to dispel rumours circulating in both Algiers and Paris about the president's condition deteriorating.
But they failed to convince media in Algeria, with many newspapers commenting about his weak health.