The government crisis center and Health Ministry previously had reported between 128 and 139 people were killed, but lowered the death toll late Thursday without giving any official explanation. The Transportation Ministry also gave a death toll of 36.
"A mistake was made in the death and injury toll because of the contradictory information that reached us," said Ayhan Cevik, mayor of the nearby town of Bilecik. "According to the latest information we have, 36 people were killed in the accident and 60 were injured."
At least four train cars overturned near the small, rural village of Mekece in Sakarya province, with most of the damage in two cars that crashed into each other. Bodies lay near the tracks as people climbed on the overturned cars looking for survivors. Darkness was hampering rescue operations, with soldiers searching the wreckage and treating the injured by flashlight.
It was not immediately known what caused the derailment of the train, a fast connection from Istanbul to the capital, Ankara. There was controversy when the line started operating June 4, with critics saying the tracks were old and could not handle the new trains.
Still, authorities said they were not ruling out sabotage.
"We are assessing every possibility," said Muammer Turker, heading the crisis center in Sakarya. He said the train was carrying 234 passengers and nine personnel.
When it derailed, the train would have been traveling at a normal speed, because the tracks near Mekece were not geared to carry high-speed cars, state railway authority deputy head Ali Kemal Ergulec said. It was not immediately known how fast the train was going when it derailed 183 kilometers (113 miles) away from Istanbul, about midway to Ankara.
"The train was a little fast going around the curves, Namik Kemal Ozden, said lying in his hospital bed, his face bandaged. "There were vibrations. My cousin was sitting next to me, we hugged each other. The windows broke and we fell to one side. We could only understand what happened once we got out."
At the scene, rescue workers were combing through the debris, looking for survivors.
Paramilitary soldiers were carrying luggage from the debris and piling it on the side of the road.
Most of the white train cars with red trim were lying on their sides. Windows were shattered.
"There were bodies lying all over the place," said Hikmet Feridun Turan, the mayor of nearby Pamukova and one of the first people to reach the site.
"Body pieces. Heads lying on the ground. I don't want anyone to ever see anything like that," he said.
The crash occurred at 7:45 p.m. (0445 GMT) and by midnight, most of the rescue efforts were winding down.
Prime Minister Recep Tayyip Erdogan canceled a trip to Bosnia scheduled for Friday and traveled to the area by helicopter.
He said authorities would likely make an announcement on the cause of the crash on Friday.
Oguz Dizer, a journalist traveling in the area, told NTV television that soldiers were on the scene to help the injured. He said he saw several bodies lying near the tracks.
"The scene is one of carnage," Dizer said. "There are people lying all over the place."
Suleyman Karaman, the head of Turkey's railway authority, said a team had been sent to the area to try and determine the cause of the crash. He quoted the train's conductor as saying the train was traveling at normal speed and that he "could not understand what had gone wrong."