Police said only that he was injured during the police operation to free the woman.
Police used Twitter earlier on Monday to warn people to avoid the station as ambulances and heavily-armed police lined up behind the train station, the daily Koelner Stadt-Anzeiger reported.
"The suspect is under control", Cologne's police said after indicating a man had been holding one woman against her will.
Cologne police said they have closed parts of the western German city's main train station because of a hostage situation.
"We are in contact with the man", police spokesman Christoph Gilles told broadcaster n-tv at the time.
"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 commandos were deployed and the busy railway station was closed off to all passengers and trains".
The woman sustained minor injuries and was treated at the scene. He wouldn't confirm local media reports that the hostage-taker had first attacked the girl before taking the other woman hostage. Police have cordoned off the entire area while Deutsche Bahn, Germany's largest railway company, has partially suspended trains passing by the Cologne station.