A crash between a bus and a train travelling at high speed in northern Belgium has killed four people, including two children, and injured five other children, officials say.

The injured children were hospitalised in a serious condition, said Lisa De Wilde, spokeswoman for the East Flanders public prosecutor's office.

The collision happened at a level crossing during the morning rush hour on Tuesday (Tuesday afternoon AEST) near the town of Buggenhout, more than 30 kilometres north-west of the capital, Brussels.

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The minibus driver and an escort were killed along with two children, 12 and 15, De Wilde said at a news conference.

She said that the cause of the crash hadn't been established. Investigators were questioning witnesses and checking security camera footage.

"What we do know is that the barrier was closed and the red light was on," she said.

An Associated Press reporter at the scene said the badly damaged bus lay toppled on its side, its front section crushed flat.

Forensic experts in protective white suits and wearing gloves were taking photos of the scene. A forensics tent was erected nearby. The train was relatively unscathed.

The train was estimated to be travelling at about 120km/h as it approached the crossing and had "no time to brake", said Frédéric Sacré, a spokesman for Belgian rail operator Infrabel.

"The impact was extremely violent," Sacré told RTBF public broadcaster.

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Federal Police spokesperson An Berger said that the bus driver appeared to have ploughed through the train barrier.

Infrabel said that the crossing was working correctly. A security camera there showed that the bus, which had nine people aboard, was still moving when the train hit it.

It's believed that 100 passengers were aboard the train and that none of them were hurt. Rail traffic in the area was halted and bus services provided for travellers. Local officials stood for a minute's silence after the news conference.

Children played basketball and rode bicycles at a school not far from the scene in this bucolic town.

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In a social media post, Interior Minister Bernard Quintin expressed "great sadness" over "the tragic accident in Buggenhout, where a school bus was struck by a train".

"My thoughts go out to the victims and their loved ones," he said.