A fire brigade spokesman confirmed six dead, but said rescue teams had not yet searched through all of the wreckage.
"There are many injured," said David Ridal, a fire brigade officer.
"There are some dead, but we do not have precise numbers because our people are devoting time to rescue those alive."
The nationality of those killed was unclear, but both Krakow and Prague are popular destinations for foreign visitors.
The locomotive and several carriages of the express train were severely damaged.
Pictures showed rescue teams climbing into mangled green-and-white train carriages that had been thrown off the rails and had become tangled in the ruins of the bridge.
"It looks terrible there. The carriages are derailed and passengers are trapped," said Jan Kucera, of the Czech railway inspectors' organisation.
Rescuers said the bridge, which was under reconstruction, may have collapsed while the train was approaching or passing underneath.
Studenka is about 350km from Prague and close to the eastern Czech city of Ostrava and the Polish border.
A spokeswoman for the Ostrava municipal hospital said ambulances and a helicopter had begun bringing in injured passengers.
"All staff have been called to service and we have freed a number of beds to make room for the injured," said Anna Vidisevska.
Mirek Topolanek, the Czech prime minister, and Donald Tusk, his Polish counterpart, were on their way to the site.