Authorities said the perpetrator has sustained life-threatening injuries.
"We need to find out what he wants, what his demands are and whether he carries a weapon", he said, adding that police weren't aware of the man's motive. Police said there was no immediate suspicion of a link to terrorism. The area in and around the station - a major transport hub - has been cordoned off.
Deutsche Bahn said the station will be closed until further notice and all traffic - including long-distance - has been suspended.
Cologne police say they have closed parts of the western German city's main train station because of a hostage situation.
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Police said they could not yet positively identify the hostage taker, who was undergoing surgery, but believed he was a 55-year-old Syrian migrant.
Reports speak of at least one explosion during the incident. Ambulances and heavily-armed police were lined up behind the train station, the daily Koelner Stadt-Anzeiger reported.
The suspect, who was badly wounded when police stormed the scene, had claimed to be a member of the Islamic State jihadist group, another police spokesman said.
A woman held hostage by the perpetrator was only "lightly wounded", police tweeted shortly after she was freed around 3:00 pm (1300 GMT).