Popular anger is growing over the poisonous waste dumped around the city, and the public outcry forced the resignation of the government last week.
On Friday, Innocent Kobenan Anaky was dragged out of his car and assaulted by demonstrators.
Joel N'Guessan, the vice-president of the minister's MFA party, said Anaky "was beaten up after being pulled out of his car by a crowd demonstrating this morning against the toxic waste ... the protesters burned his car. He is seriously injured."
The health ministry said on Friday the number of people who had died from inhaling noxious fumes from the waste rose to seven.
More than 23,000 people have sought treatment at hospitals for vomiting, nausea and breathing difficulties.
The surprise resignation of the cabinet injected more uncertainty into an already tangled political outlook for the country, which has been split in two since a brief 2002-2003 civil war.
Charles Konan Banny, the prime minister, said on Thursday that a French company, Tredi International, would begin to remove the waste from Sunday and he said the government was working to have it sent abroad.
"As the waste is gathered up, the soil will be treated in order to eliminate any trace of pollution," he said in a televised address.
Ivorians have been seeking
medical aid from the Red Cross
Banny said it was "not necessary" to state the chemical composition of the waste.
But foreign experts brought in to test the viscous substance, unloaded from a Panamanian-registered ship at Abidjan port last month, have said it appeared to contain hydrogen sulphide, which can be deadly in high concentrations.
The Ivorian authorities have arrested seven Ivorians and one Nigerian in connection with the dumping of the waste, which was deposited in open-air sites around the city.
Banny said national and international inquiries would be conducted to find out how the waste was dumped, and four senior officials, including the heads of Abidjan port and the customs service, had been suspended.
He said tap water remained safe to drink, but fishing had been banned in the Abidjan lagoon and livestock near the sites where the black sludge was dumped were being observed.