Two executives of Trafigura Beheer BV, director Claude Dauphin, and manager for West Africa, Jean-Pierre Valentini, were charged under toxic waste and poisoning laws and remanded in custody, the chief of staff to the justice minister, said.
Seven people have died and thousands became ill after inhaling toxic fumes from waste originally unloaded at Abidjan port last month from the Probo Koala, a tanker chartered by Trafigura.
Trafigura described the waste unloaded from the ship as residue washings - a mixture of petrol, water and caustic washings - from the petrol blend stock cargo the ship had been carrying. The company said it had hired an Ivorian firm, Tommy, to dispose of it properly.
The waste was dumped at 11 open air sites around the economic capital of the West African country causing vomiting, stomach pains, nausea, breathing difficulties, nosebleeds and migraines among thousands of local residents.
Hospitals have provided free treatment to 44,000 people in the past few weeks.
Experts who tested the substance said it appeared to contain hydrogen sulphide which could be deadly in high concentrations.
Trafigura said in a statement it was "shocked" by the arrest of the two men.
Abidjan's hospitals have had to
treat 44,000 people
"The two men, who were part of a humanitarian mission from the company, were originally stopped as they were about to board a plane on Saturday 16 September," the company said in a statement.
They were arrested after an appointment with a judge whom they saw of their own free will, it said.
Eight other people, including the heads of Tommy and two other Ivorian companies as well as customs officials, have also been arrested over the scandal.
A French waste removal company began a clean up operation on Sunday at the main rubbish dump, the worst affected site in Abidjan.
Removing the waste is expected to take two weeks.
A Dutch junior minister has been accused by the public prosecutor of misinforming parliament in the Netherlands over the toxic waste crisis, according to Tuesday's edition of the newspaper, De Volkskrant.
Peiter van Geel told deputies last week that the waste on freighter was not dangerous and thus did not require an export permit. The prosecutor's office said that it was already known when the state secretary made his statement that the waste was toxic, and that a decision would be made by week's end on whether to launch a formal investigation.