Slovak police said that about 80 passengers were estimated to be onboard, but didn't immediately offer more details.
Interior Minister Matúš Šutaj Eštok said two of the injured were in critical condition while the other injuries weren't serious.
Images from the collision showed the front part of one engine badly damaged, while the other train derailed.
Authorities have opened an investigation into the cause of the crash. Šutaj Eštok suggested human error might be to blame.