Four people who were seriously injured were taken away by helicopter and seven others required surgery, while 31 suffered minor injuries in the crash near the western Czech town of Domazlice, the regional rescue service said.
He said human error was likely to have caused the crash and that the high-speed train had failed to stop at a designated location.
“The situation is serious,” he added.
Police confirmed at least three people died in the tragedy which happened shortly after 8am in the town of Milavce.
TV footage on Czech television showed the smashed driver’s cabin of the fast train‘s locomotive, as well as the front part of the local train.
Commander Jaroslav Hrdlicka of the regional fire department said rescue workers were still looking for one missing person in the wreckage.