Though the transport ministry's crisis centre had earlier put the death toll at 139, no reasons were given for the subsequent revision in the figure.
"The initial death toll was 28 and now it has gone up to 36," a crisis centre spokesman said. The Turkish Prime Minister Tayyip Erdogan also put the death toll at 36.
There were conflicting reports on the number of those injured which was earlier put at 57.
The transport ministry put their number at 43, while the governor of the nearby province of Bilecik was quoted by the Anatolia news agency as saying that 60 people were injured.
The packed train from Istanbul to capital Ankara derailed near Pamukova town in Sakarya province.
There were 234 passengers and nine crew aboard the train when the accident occurred.
Erdogan said he had cancelled a trip to Bosnia-Hercegovina, scheduled for Friday, following the train accident.