The allegations came at the start of a trial in which the firm is accused of breaking Dutch export and environmental laws and forging official documents.
Tens of thousands of people in Ivory Coast said the waste made them ill.
Trafigura rejects the charges. It denies the waste was dangerous, or that it knew the chemicals would be dumped.
Among those standing trial is an employee of Trafigura and the Ukrainian captain of the Probo Koala, the ship that exported the waste from the Netherlands.
Neither were present as the trial opened in Amsterdam on Tuesday.
The city of Amsterdam and Amsterdam Port Services (APS), are charged with not preventing the export of dangerous waste.
The waste was pumped back onto the Probo Koala after APS said it was more toxic than initially thought and asked for a higher price to dispose of it.
Trafigura, a multi-national oil trading company, eventually hired a local Ivorian firm to do the disposal. The chemicals were dumped in waste disposal sites around Abidjan, Ivory Coast's biggest city.
The head of the local contractor was sentenced to 20 years in prison in a trial in Ivory Coast in 2008.
Shortly after, tens of thousands of people complained of becoming ill. A UN report last year suggested a strong link between at least 15 deaths and toxic waste dumps.
"The waste is thrown over the fence, dumped in a third world country," public prosecutor Luuk Boogert said at the trial on Tuesday.