The train was travelling from the Netherlands to Ghent’s seaport when it derailed as it changed tracks between the towns of Schellebelle and Wetteren at about 02.00 a.m.
Six of the train’s 13 cars derailed and three caught fire, setting off a series of explosions.
It is unclear how the two people died.
More than 300 people were evacuated from the area.
Local official Jan Briers said: “Everything is well organized, I think, and right now, there is no reason to increase the safety zone.”
The fire was brought under control later on Saturday morning but residents were advised to keep their doors and windows closed.
The commander of the Ghent fire brigade, Christian van de Voorde, said the best way to limit the spread of toxic chemicals had been to let the fire burn out.
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