"A female hostage has sustained light injuries and is being tended to".
"Police measures are continuing", Cologne police wrote on Twitter just after the special unit assaulted the shop.
It is not yet clear why the man took the woman hostage.
The police said in a subsequent tweet that there had been no shots fired and there were no immediate reports of casualties.
The woman was released and is reported to have minor injuries, while the man was taken to hospital in a serious condition.
"We also do not rule out a terrorist attack", Brauns said.
Authorities ordered an evacuation of the station, which is a main hub for rail traffic across Germany and western Europe. The entire station, one of the biggest in the country, was evacuated and closed off as well as Breslauer Platz square behind the station.
Gilles said specially-trained officers were talking to the hostage taker, who hadn't been identified.
'We have indications that one man is holding one woman, but we haven't been able to really get close, ' Schulte said.
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.
Deutsche Bahn cancelled or delayed train services in Cologne during the stand-off. Police would not speculate on whether the hostage situation was terror-related.