A team of 25 waste removal experts began pumping the hazardous black sludge from the city's main rubbish dump, one of up to 14 sites across Abidjan that the UN says have been contaminated.
The chemical refuse is a byproduct of a fuel shipment apparently dumped illegally in late August by a contractor working for a Dutch commodities company.
The Ivorian government said that at least six people had died from exposure to the waste, while thousands have sought treatment at hospitals.
A UN report said the waste contains a chemical called hydrogen sulfide which, in large doses, can kill people.
The waste was discovered by residents who began complaining of a nauseating stench and persistent health problems such as vomiting, sore throats and headaches last month.
The waste removal operation comes a day after a new 36-member cabinet was appointed. The ministers of transport and environment were replaced and several new posts were created.
The entire cabinet resigned last week as a result of the dumping scandal, but almost all were reappointed to their posts.
Rubbish has filled the streets of Abidjan as waste sites have been blocked off.
Protests about the dumping turned violent on Saturday, when the house of a port official was burned down and the deposed transport minister attacked.
Henri Petitgand, a spokesman for the French company removing the waste, said that the clean-up operation was expected to take two weeks.
Donor countries are helping the government pay for the clean-up but Patrick Achi, the infrastructure minister, said those responsible for the dumping were expected to reimburse the costs.
Under the international Basel agreement, which was signed in 1989 to protect poor countries from the dumping of hazardous waste, a country found responsible for the dumping of toxic waste must pay for its removal.