Cabin crew scheduled to work on some flights "have not wanted to carry out their assignment", a spokesman for the company told AFP.
He refused to be drawn on numbers but said none of the flights destined for the region had ultimately been left short-staffed.
"In the end, all these flights left with the usual number of crew and with teams that had the usual level of qualifications, according to the regulations," he said.
Air France operates daily flights to Guinea and Nigeria and a service three times a week to Sierra Leone.
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Ebola has killed 1,229 people so far this year in west Africa, the worst outbreak ever of the virus.
Yesterday one Air France union, SNGAF, launched a petition calling for the "immediate end to flights to countries hit by the Ebola virus".
She said that hygiene measures implemented so far were "stop-gap" and that crew had "no idea if we are carrying a victim or if we ourselves are carriers of the virus".
Flight crews for Air France can request to be withdrawn from a scheduled flight if they believe their health or life is in "grave and imminent danger", with the team then usually replaced by a reserve team.