Thousands of people queued at hospitals and health centres to get treatment for symptoms related to the toxic fumes.
More than 500 tonnes of toxic waste that were dumped last month on open-air rubbish tips in Abidjan, killing seven people, causing thousands to fall ill and provoking widespread riots.
The substance at the heart of the crisis is a mixture of oil residue and caustic soda used to rinse out the tanks of a Greek-owned cargo ship, causing nausea, rashes, fainting, diarrhoea and headaches.
A French company is carrying out the clean-up operation, which is expected to take two weeks.
The clear-up began at Abidjan's main rubbish dump, the site worst affected by the foul-smelling sludge.
"Technically it is not very easy, we are talking about toxic waste so we have to be very careful," said Francois Salbaing, from France's Seche group.
The 400 metric tonnes of waste contained a mixture of gasoline, water and caustic washings.
The government's slow reaction to the crisis so enraged Ivorians that the cabinet was forced to resign and the government reshuffled.
The company which chartered the ship which transported the waste, Trafigura Beheer BV, says it informed the Ivorian authorities that the waste should be disposed of correctly.
An inquiry is under way and eight people have been arrested so far. "The polluters will pay," said Ivory Coast’s Prime Minister Charles Konan Banny.
The scandal led to the resignation of the whole government on September 6 but all the ministers except for two - transport and environment - have returned to office.