The six-car Sanyo Railway limited express train hit a truck near the station in Takasao in Hyogo prefecture, NHK News reported.
Local police are investigating the cause of the accident, officials said.
The first and second cars derailed and the train traveled for another 557 feet before it crashed into a station platform, officials said.
NHK said the train's driver was seriously injured.
The accident interrupted some of the railway's passenger service, China's state-run news agency Xinhua reported.
Transportation officials said the alarm signaling system designed to detect obstacles around the crossing was working.