Jan Briers, governor of eastern Flanders, gave the death toll to the Belga news agency after the accident and blaze prompted authorities to evacuate nearly 300 people from their homes.
The accident happened around 2:00 am (0000 GMT) between the towns of Schellebelle and Wetteren, said Infrabel, the entity responsible for the Belgian railway network.
Six of the train's 13 cars derailed and two were on their side.
The blaze led to a series of explosions in the railway cars, then a spectacular strip of fire spread over hundreds of metres prompting authorities to evacuate residents living near the site of the accident.
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The blaze was under control by late morning but residents were told to keep their doors and windows closed.
The causes of the accident remained unclear. The cars derailed as the train changed tracks and observers said it might have been travelling too fast.
The train came from the Netherlands and was bound for Gent-Zeehaven, the city's seaport.
Train services between Schellebelle and Wetteren were disrupted and problems were expected for two days, with buses laid on to transport passengers.
Two similar accidents involving goods trains carrying tanks of toxic products occurred in Belgium in May 2012.