The dead fish, an endangered species, were seized near Paris in parcels sent from Guinea and bound for Hanoi probably for sale as so-called aphrodisiacs.
The French President is the first Western leader to visit Guinea, where more than 1,200 have died from the disease since the March outbreak.
Development secretary Annick Girardin is in Guinean capital Conakry to visit Ebola units and discuss France's role in halting epidemic.
Unions say management has promised no action will be taken against pilots or cabin crew not wishing to fly to affected regions.
Foreign ministry says trips to four countries hit by Ebola fever outbreak - Liberia, Guinea, Sierra Leone and Nigeria - should be put on hold.