It wasn't immediately clear how he sustained the injuries.
Authorities have since said the situation is "under control" and the teenage women taken hostage is receiving medical treatment for light injuries.
Police set up a webpage where members of the public could upload pictures and video related to the incident, while their own investigations were "at full pitch".
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Deutsche Bahn said the station will be closed until further notice and all traffic - including long-distance - has been suspended.
But shortly afterwards police commandos stormed the pharmacy with stun grenades.
"We have indications that one man is holding one woman, but we haven't been able to really get close", Schulte said.
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German police have stormed a pharmacy in Cologne's central railway station, freeing a woman who had been held hostage by a man for two hours.
Travellers were ordered to evacuate the large central station, which sits on Cologne's Dom Platz beneath the city's historic cathedral early Monday afternoon. A spokeswoman said officers had forced their way into a pharmacy where the suspect was, adding that the hostage-taker's motives were unclear.
Special police operate outside the Cologne, western Germany, train station Monday, Oct. 15, 2018. Police would not speculate on whether the hostage situation was terror-related.
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