Packed into rows of cylindrical containers, the waste left Abidjan's port just before midnight on Friday aboard the MN Toucan, a vessel belonging to the French shipping company, Maritime Nantaise.
Franck Ouvray, the ship's captain, said it would take about 10 days to transport the first of four loads of the waste to Le Havre, France.
Tredi International, the French company contracted by the Ivorian government to clean up the waste from 17 sites around Abidjan, has removed about 5,000 tonnes of toxins and surrounding dirt since September 17.
Henri Petitgand, the Tredi Spokesman, said clean-up crews had not finished and were still working at two sites. He said once the containers get to France, it will take about two weeks to neutralise their toxic contents.
The waste was offloaded in Abidjan on August 19 from the Probo Koala, a vessel chartered by the Dutch commodities trading company, Trafigura Beheer BV.
Trafigura officials say the ship was carrying a cargo of gasoline and stopped in Abidjan to dispose of the content of the ship's waste tanks, known as "slops."
Trafigura says the waste disposed of in Abidjan was a mix of gasoline residues, water and caustic sodas used to clean slops.
Ivorians in a protest in Abidjan
last September over the waste
UN experts, however, say the waste that was dumped in Abidjan contained hydrogen sulfide, which in concentrated doses can kill humans.
Trafigura officials say it is a mystery how the hydrogen sulfide got there, as caustic sodas typically used to clean slops cannot produce the toxic substance, according to Trafigura.
Ivory Coast's Health Ministry says 10 people have died in areas where the waste was dumped.
The ministry says more than 60 people have also been hospitalised and more than 100,000 have sought medical treatment.
Ivory Coast's government is investigating the scandal but has yet to announce any findings.