Umatgirei Kartoev told RIA Novosti his son, Tarkhan, died June 29 in a prison outside the city of Yekaterinburg after being beaten.
Last year, a Russian court sentenced Tarkhan Kartoev, 40, to seven years in jail for planting explosives with nine other people to derail the train.
Prison authorities told the father his son died from cardiac arrest in a telegram.
"There are no traces of violent death on the body," Yelena Tishchenko of the region penitentiary service told RIA Novosti. "Despite efforts to resuscitate him that lasted 30 minutes, there was no heartbeat."
But the father said pictures show a body that looks like it is covered in burns and contusions, and a deep line of stitches is visible on his head.
He submitted the photos to the human rights group, Memorial.
"In my non-professional opinion, this man was tortured, although it is impossible to verify it," Timur Akiev of Memorial told RIA Novosti.
Investigators said they would open a new investigation into the death.