The Dutch-based company with London offices paid an Ivorian company to dump the waste in Abidjan. Thousands of people sought hospital treatment.
Amnesty and Greenpeace say a three-year investigation shows the UK and Dutch authorities failed to stop the dumping or hold Trafigura to account.
Trafigura denies any wrongdoing.
One of the world’s largest transport companies, it has always argued the waste was not dangerous.
It says a new report – The Toxic Truth, based on Amnesty and Greenpeace’s three-year investigation – contains significant inaccuracies and misrepresentations and oversimplifies difficult legal issues.
In August 2006 families in Abidjan, the commercial port of Ivory Coast, woke to a foul smell, with toxic fumes wafting into their homes, says BBC Africa analyst Martin Plaut.
The company denies the waste could have caused the reported illnesses, and said it had paid a local company to properly and legally dispose of the waste.
The exact risk to humans from the waste has been heavily disputed.
Series of payments
Amnesty and Greenpeace say the Trafigura case exposes how international law needs to be updated to cover companies that operate across borders.
“One company has been able to take full advantage of legal uncertainties and jurisdictional loopholes, with devastating consequences,” said Greenpeace International Executive Director Kumi Naidoo.
Probo Koala, the ship carrying the waste, had docked in Amsterdam. But when the cost of treating it was considered too high, the Dutch allowed the ship to leave port and it then went on to be unloaded in Ivory Coast.
A Dutch policeman warned the London office of Trafigura that the ship was carrying chemical waste, the report says.
The policeman – quoted anonymously – said: “I never realised that Trafigura would leave the waste in Africa. I thought that if I would continue making phone calls… the company would not dump the waste at sea but keep the waste onboard instead until the ship would return to Europe.
“The reason why I did not raise the issue higher up is because my experience is that it would not be acted upon.”
Trafigura has made a series of payments in relation to the case without admitting liability.
In 2007, it paid an estimated $160m (£100m) to the Ivorian government in compensation.
Two years later it also agreed to pay $45m to individual claimants in an out-of-court settlement before the case came to trial in London – after a group of British lawyers, Leigh Day and Co, organised a class action involving 30,000 Ivorians.
In July 2010, a Dutch court found Trafigura guilty of illegally exporting toxic waste from Amsterdam and concealing the nature of the cargo, fining the company 1m euros ($1.3m; £800,000).
Source- BBC © 2012