The Turkish state news agency, Anatolian, said the bomb, which exploded as the train passed, flipped over 12 carriages, leaving eight unusable, and wrecked 20 metres of track in the eastern province of Mus.
Officials said the bomb may have been activated by remote control.
Attacks against security forces, civilians and property in the mainly Kurdish east and southeast have escalated in recent months, while Istanbul has also been targeted with bomb blasts claimed by a group linked to the outlawed Kurdistan Workers' Party (PKK).
A bomb exploded in a dustbin in central Istanbul this week, which has not been claimed, while on Friday a bomb in the eastern province of Van injured three and smashed the windows of a meteorological centre.
The PKK, considered a terrrorist organisation by Ankara, the European Union and the United States, has been blamed for more than 30,000 deaths since the start of its campaign for a homeland in 1984.