In total, the vehicle was carrying seven pupils from a school for children with learning disabilities, authorities told a press conference.
The other five children on board were taken to a local hospital where they remained in stable conditions, having sustained severe injuries, prosecutors said.
Their lives were not in danger, added police spokeswoman An Berger.
“I can’t imagine what the parents are going through,” Magda, a woman in her 40s whose son was at the station waiting for the train involved in the crash when the collision occurred, told AFP.
No one on the train was hurt.
European Commission chief Ursula von der Leyen joined in the stream of commiserations from politicians, saying she was “heartbroken” by the collision.
“My deepest condolences go out to the victims’ families and their loved ones,” she posted online.
“Today, Europe grieves with Belgium.”