The BBC Shanghai left the northern French port of Cherbourg after approval from local officials, who carried out an inspection on Wednesday, and was due to arrive by the end of the year in New South Wales state.
It was laden with radioactive waste from spent nuclear fuel that Australia sent to France for reprocessing in four shipments in the 1990s and early 2000s, the Australian Nuclear Science and Technology Organisation (ANSTO) said Friday.
The reprocessing involves removing uranium, plutonium and other materials, with the remaining substances stabilised in glass and stored in a container.
"The container will be placed on a nuclear-rated ship, brought to an Australian port, and trucked to Lucas Heights (nuclear facility) with an appropriate security operation," ANSTO said in a statement.
"The ship was selected by (France-based nuclear company) Areva, and after a full inspection carried out by both French maritime safety authorities and by the French nuclear safety regulator on Wednesday 14 October, the ship's seaworthiness was confirmed and certified."
Greenpeace, French environmental campaign group Robin des Bois (Robin Hood) and a leading green lawmaker called for the shipment, sent by Areva, to be halted.
"Areva, almost bankrupt, are using a dustbin ship to carry waste, without any serious inspection!" Denis Baupin a senior lawmaker with the French green party, tweeted.
Greenpeace Australia Pacific said the ship -- owned by German firm BBC Chartering -- was an "environmental disaster waiting to happen", claiming that the Shanghai was "blacklisted by the United States because of its safety record".
'Staggering number of flaws'
But Areva's external relations director Bernard Monnot said the ship was "not banned from ports in the United States but banned from transporting material for the American government".
Nathalie Geismar from Robin des Bois said other ports had found it had a "staggering number of flaws".
Authorities in the Manche (Channel) region, who inspected the 14-year-old ship, said they found no problems to prevent it from sailing or put crew or cargo in danger.
Monnot said small flaws identified during inspection, such as a malfunctioning thermometer in a hold, had been put right.
The two containers of waste came from the company's reprocessing plant in Beaumont-Hague, near Cherbourg.
ANSTO said the material would be kept at the Lucas Heights facility in southern Sydney until a nuclear waste dump site, which has yet to be chosen, is found and constructed.
Greenpeace called for assurances from the Australian government that the waste would be safely stored.
"We want to know what safety precautions the Australian government will put in place when this ship arrives on our shores," Greenpeace Australia Pacific Emma Gibson said in a statement.
"We also want assurances from the ANSTO that the waste -- which will take years to degrade -- will be safely stored."
Lucas Heights houses Australia's only nuclear reactor, with the facility mostly used for nuclear medicine and research.