The government, which initially put the death toll at 139 subsequently revised the figures, saying the mistake was due to "contradictory information."
Despite reports that the modified tracks were not safe for the high speed train service which was started last month, officials said the train, carrying 230 passengers from Istanbul to the capital Ankara, was not travelling fast at the time.
At least four carriages overturned, and ambulances and paramedics from neighbouring villages were requisitioned to assist in rescue and relief operations. One report said local people were seen hammering on the windows of carriages to see if anyone inside was still alive.
"The scene is one of carnage... There are people lying all over the place," a journalist at the site told a local television channel.
"We came to the site of the accident five minutes after it happened. People, parts of bodies were strewn all over the place," Feridun Turan, mayor of the nearby town of Pamukova, told Turkey's NTV news channel.
Prime Minister Recep Tayyip Erdogan - who cancelled a visit to Bosnia-Hercegovina to visit the scene - put the death toll at 36, and said 68 people had been injured.
Announcing an investigation into the accident, the head of Turkey's railway authority Suleyman Karaman quoted the conductor as saying the train was travelling at a normal speed and he "could not understand what had gone wrong".
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