Authorities said the perpetrator has sustained life-threatening injuries.
During negotiations over the hostage, the man asked for the release of a Tunisian woman and demanded to be allowed to leave the train station unimpeded, Rueschenschmidt told reporters.
There had been reports of shots fired, although police later said this was not the case.
Cologne's central station itself is a major interchange for trains across Germany and Western Europe.
Deutsche Bahn said the station will be closed until further notice and all traffic - including long-distance - has been suspended.
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Following a hours-long standoff, German police have finally apprehended an assailant who took hostage a woman near Cologne central station. Police believed the hostage-taker is armed.
'We have indications that one man is holding one woman, but we haven't been able to really get close, ' Schulte said.
Police say officers have contact with the man and that trained hostage negotiators are working on the case.
There was a full evacuation of the station, one of Germany's biggest transport hubs. Ambulances and heavily-armed police were lined up behind the train station, the daily Koelner Stadt-Anzeiger reported. Police said the situation was considered "under control" and there was no immediate suspicion of a link to terrorism.
Police negotiated with him in a bid to defuse the tense situation and ascertain his motive, then stormed the pharmacy around 3:00 pm (1300 GMT).