The high-speed passenger train, which hit another carrying freight in the centre of the country, belonged to the private RegioJet company.
A passenger train has collided head-on with a freight train in the Czech Republic.
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At least four people were killed and 23 others injured, officials said early Thursday.
The crash took place late Wednesday night in the city of Pardubice, some 100 kilometers east of Prague, according to Interior Minister Vít Rakušan.
Transport Minister Martin Kupka said the main track between Prague and the eastern part of the country had to be closed while authorities investigate the collision.
“We can't and won't speculate about the cause of the accident," Kupka said.
The private RegioJet company owns the train.
Rakušan said none of the injured was in life-threatening condition.
The state-run train company, Czech Railways, said it's likely the track will remain closed for the entire day “due to the extent of the accident.”
Rescuers said more than 300 passengers were on board the high-speed train heading for the city of Kosice in eastern Slovakia.
The dead were not immediately identified. The drivers in both engines survived, the local CTK news agency said..
The corridor in Pardubice, where the trains collided, is vital for Czech Railways. It said the line will also likely be closed tomorrow.
Prime Minister Petr Fiala called the crash a big tragedy and offered his condolences to the families of those killed.