The BBC Shanghai is due to reach Australia by 27 November.
French officials said an inspection had revealed no problems that could prevent the ship from sailing.
The 25 tonnes of nuclear waste comes from Areva`s reprocessing plant in Beaumont-Hague, near the port of Cherbourg, from where the ship set sail on Thursday.
Yannick Rousselet, of Greenpeace France, said the BBC Shanghai "should not be used" to transport the nuclear waste.
Nathalie Geismar, of French environmental group Robin des Bois, said that other ports had found a "staggering number of flaws" in the 14-year-old ship.
Shortly before the cargo ship set sail, French Green MP Denis Baupin tweeted (in French) that Areva was "using a dustbin ship to carry waste, without any serious inspection".
The Australian Nuclear Science and Technology Organisation (Ansto) said a full inspection of the ship had been carried out by both French maritime safety authorities and by the French nuclear safety regulator on 14 October.
"The ship`s seaworthiness was confirmed and certified," a statement said, adding that the ship had been chosen by Areva.
The waste comes from spent nuclear fuel sent from Australia to France for reprocessing in the 1990s and early 2000s, Ansto said.
Under French law, the waste from the operation is required to have left the country by the end of 2015.
The BBC Shanghai is registered in Antigua and Barbuda.
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