The collision occurred late yesterday when the fast-moving passenger train slammed into the back of a slow freight train which was travelling on the same track for unknown reasons. The crash happened at Hermalle-sous-Huy, near the eastern town of Liege.
Authorities said lightning and flood damage caused by the heavy storms that have affected western Europe over the past week were being explored as a possible cause of the crash.
"All my condolences for the families of the victims... and a fast recovery to the injured," Michel said on Twitter.
Although investigators were hard at work, finding the cause "would be difficult", warned a spokeswoman for the prosecutor's office in Liege.
"The passenger train is really in a bad way, it's stunning," said Francis Dejon, mayor of the municipality of Saint-Georges-sur-Meuse, where the crash took place.
"The front carriage is scrunched back up on itself. We were very lucky not to have more victims," he told the Belgian news agency Belga.
Investigators believe the freight train was travelling at about 10-15kph at the time, said Brigitte Leroy, a spokeswoman from the prosecutor's office.
The crash killed the driver of the passenger train, authorities said. Of the nine injured, some were in critical condition, they added.
"Two of the six carriages derailed and are lying on the tracks," the Infrabel railway infrastructure company and the National Railway Company of Belgium (SNCB) said in a joint statement.
Infrabel spokesman Frederic Sacre said investigators would look carefully at a report of lightning on the tracks some 90 minutes before the crash.
Yesterday evening, SNCB said lightning had caused signal problems near the site, but that the incident was over.
In 2008, there was crash at almost the exact same location in which 42 people were injured. That incident was later blamed on human error and a power failure.
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