Although the airline suspended services to neighbouring Sierra Leone, which is also suffering from the Ebola outbreak, it has continued flights to Conakry.
Other airlines, including British Airways, have suspended flights to the west African countries hit by the virus.
They “should not be isolated and should remain open”, Hollande said, calling for international help to be stepped up.
More than 3,000 people have been killed by Ebola by the end of the year.
Hollande assured Condé of France’s “total solidarity” for Guinea where 1,074 have been infected and 648 died.
The French government has alloevared 35 million euros and would soon a third Ebola clinic, sending 25 French doctors to help fight the epidemic.