The intercity express train appears to have crashed into an empty container unit at the western end of the Great Belt bridge, between the islands of Zealand and Funen.
The accident struck around 7:30 a.m. on the busy Storebaelt bridge that connects the central islands of Zealand and Funen, according to the Danish Broadcasting Corporation. The number of injured is as yet unknown.
Rail network officials said debris from a freight train - possibly a tarpaulin - hit a commuter train during a heavy storm, forcing it to brake suddenly.
Denmark's TV2 reported that eight people were injured and showed images of the freight train.
134 people were reported to be aboard the train, including three crew.
The 18-kilometer (11-mile) bridge, which is part of infrastructure linking Denmark and Sweden to Germany, carries around 21,000 train passengers and more than 27,000 vehicles each day.
The passenger train had departed from the city of Odense, on the central island of Fyn.More news: Federer triumphs over Serena in 'super cool' Hopman Cup encounter
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"Ordinary Danes on their way to work or heading home from the Christmas holidays have had their lives smashed", Prime Minister Lars Loekke Rasmussen said in a statement of sympathy that was translated by the Associated Press.
The Carlsberg beer company confirmed that freight train operator DBS was carrying their goods in the train.
Cars wait after the Great Belt Bridge has been closed in both directions due to a train accident, in Denmark, on January 2, 2019.
"Our thoughts are with relatives and we are doing all we can and what is practically possible, to assist clients and their relatives", he said.
The cause of the crash is still under investigation.
The government agency responsible for Danish railways said on Twitter that no further trains would cross the Storebaelt link on Wednesday, adding it was aiming to allow train crossings to resume Thursday.