Friday's ruling is the first time Trafigura has faced criminal charges over the toxic waste scandal.
The company said it would study the court's decision with a view to filing an appeal, and said it maintained that its employee had done nothing wrong.
Trafigura has denied that the waste they carried caused any illness, but paid out $50m in compensation to 31,000 people in the Ivory Coast in September 2009.
"Amnesty is extremely concerned that the long term impacts of the waste haven't yet fully been considered"
It also agreed in 2007 to a $198m out-of-court settlement with the Ivory Coast government which exempted it from legal proceedings in the West African country.
People in Ivory Coast greeted Friday's ruling as a moral victory.
"Finally, Trafigura has been called out in a court of law," Eliance Kouassi, president of the National Federation of Toxic Waste Victims in Ivory Coast, said.
"It's a real victory for us," he said.
Benedetta Lacey from Amnesty International in London told Al Jazeera that the ruling was a "significant step" that sent out a strong message to multinationals.
But she added that for Trafigura this case should not be the "end of the story".
"Victims in the Ivory Coast continue to complain of health effects. The areas where the waste was dumped haven't been fully decontaminated," she said.
"Amnesty is extremely concerned that the long term impacts of the waste haven't yet fully been considered."
"There are impacts and conducts in this case that Holland hasn't fully considered. We're calling on states to do all they can to ensure that multinationals do respect human rights when their activities cross borders."
'Beginning of justice'
Marietta Harjono, a spokeswoman for Greepeace, described the ruling as the "beginning of justice".
"The next logical step is that Trafigura gets sued for the dumping in Ivory Coast."
In July 2006, caustic soda and petroleum residues on board the Probo Koala were prevented from being offloaded for treatment in the port of Amsterdam and redirected to Abidjan, where they were dumped on Ivorian city's waste tips.
The waste, slops from the cleaning of fuel transportation tanks, was pumped back into the Probo Koala after Amsterdam Port Services, a waste treatment company, demanded a higher price for treatment as it was more toxic than previously thought.
Trafigura declined to pay the increased price.
Amsterdam Port Services and its director Evert Uittenbosch were cleared of charges of "leaving dangerous waste in the hands of someone not qualified to process it".
Judges also dismissed charges against Amsterdam municipality, saying it was immune from prosecution as it was exercising its executive functions.