Five more people were hurt in the southern town of Nove Zamky, which is located 68 miles east of Bratislava, according to officials.
Video footage showed the train’s engine on fire, and railway officials reported that the bus had sustained significant damage.
According to railway company ZSSK, none of the train passengers were among the deceased.
The injured were treated at hospitals in nearby towns and cities because the local hospital was closed due to flooding brought on by heavy overnight rains.
According to Czech Railways, the train driver—a citizen of the Czech Republic—escaped with minor burns. Four other people were hurt while riding a train.
The crossing where it occurred is gated, and authorities are investigating.
Shortly after 5 p.m. local time (4 p.m. BST), more than 100 passengers were on the Eurocity service when the incident occurred, according to ZSSK.
It was traveling from Budapest, the capital of Hungary, to Prague, the capital of the Czech Republic.
Numerous stranded travelers were reportedly being bussed to the Hungarian border town of Sturovo, according to ZSSK.
The primary train line that connected Budapest and Bratislava has been shut down.
According to authorities, Interior Minister Matus Sutai Estok is on his way to the scene of the incident.
