Eyewitnesses said around 6:45 a.m. ET a man entered a pharmacy at Breslauer Platz, near the backside of the train station, and reportedly took one person hostage.
"Eye-witnesses reported hearing shots, others spoke of smoke bombs, but we can not confirm any of that so far", a police spokesman told news channel NTV.
Local media say the incident does not appear to have been terror-related.
German police say they've freed a woman who had been taken hostage in Cologne's main train station and have her captor in custody.
Police tweeted that the hostage was slightly injured and was now being treated.
The square behind the station was closed.
Hostage held at Cologne main train station
German railroad operator Deutsche Bahn tweeted that some of the station's tracks were shut down temporarily and trains were being canceled or delayed.
DW's Dana Regev was at the scene and watched as negotiation crisis units.
Mr Gilles said specially trained officers were talking to the hostage taker, who had not been identified.
Two explosions were heard in the area during the hostage rescue not long after elite counter-terrorism team (SEK) rushed to the pharmacy building, NTV broadcaster reported.
Police on Twitter told people to avoid the station.
A male suspect sustained life-threatening injuries in the incident.