The passenger train had departed from the city of Odense, on the central island of Fyn and was heading to Copenhagen.
Local media reports suggest that bad weather caused a tarpaulin cover to blow off a cargo train and in front of the passenger train, which forced the train to brake suddenly. "We flew down onto the floor, and then the train stopped", she told Danish public broadcaster DR.
Occurred as Storm Alfrida hit DenmarkWhilst it is too early to determine the exact cause of the crash, the incident coincided with the arrival of Storm Alfrida, which has today brought high winds and water levels to the south of the country.
A Carlsberg spokesman said a freight train operated by DB Cargo and carrying goods for Carlsberg had been involved in the accident.
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The Storebaelt bridge is part of bridges and tunnel link between the Danish islands.
Denmark's TV2 showed images of a freight train with the tarpaulin that covered the train torn in pieces.
A preliminary investigation by the Danish Accident Investigation Board showed a trailer had blown off a freight wagon onto the oncoming tracks, a spokesman said.
Police urged passengers to contact relatives and tell them if they were safe and urged people not to share photos or videos of the accident. He said the operator "will contribute everything that we can to the investigations".
Road traffic resumed on Wednesday with a reduced speed limit.