Officials gave no immediate reason for the accident, but observers and survivors blamed it on speeding along old tracks.
Turkish Prime Minister Recep Tayyip Erdogan, who immediately went to the site after cancelling a planned trip to Bosnia-Hercegovina, said 36 people were killed and 79 others injured.
"All the other figures are baseless," he told reporters when asked about an earlier death toll of 139 given out by a crisis centre in Ankara.
All five carriages overturned when the train -- with 234 passengers and 12 crew -- derailed near Pamukova town in Sakarya province on what appeared to be straight tracks with no visible hard turns, an AFP correspondent at the scene said.
Aided by spotlights, dozens of rescue workers and locals worked through the night combing the area after clearing out the dead and the injured from inside the carriages.
Bulldozers and a crane were brought in to lift the toppled carriages and check underneath for survivors or casualties as police and paramilitary troops threw up a security cordon around the area.
The Anatolia news agency initially said rescuers were trying to extricate a person trapped between the carriages, but one of the rescuers, Halil Sayin, told NTV television none of the teams had found a survivor among the debris.
Anatolia quoted anonymous railway authority officials as saying that most of the casualties were in the first two carriages and that passengers in the remaining carriages escaped unhurt.
A fireman at the scene told Anatolia that victims were either crushed to death or suffered cuts from flying glass. The injuries were also mostly caused by broken glass, another rescuer said.
It was not immediately clear what caused the train to derail, but a railway engineer at the crash site pinned it down to speeding, claiming that the train was running at 140 kilometres (87 miles) an hour on a track where trains used to travel at between 70 and 80 kilometres per hour.
"The speed was not appropriate. The infrastructure is old and could not cope with the high speed of the train," he said on condition of anonymity, adding that the last carriage jumped the track, pulling the others after it.
One survivor appeared to corroborate his words.
"Fifteen minutes before the accident, I was going from the restaurant back to my carriage and I saw a speedometer between the two carriages which read 132 kilometres," Abdulkadir Cagriguler told NTV.
Another survivor, Orcun Agabey, also said he felt the train speeding and shaking a lot, making it difficult for him to even stand up.
"Before the crash, our carriage started shaking violently, leaned to the right and we went on like that for a while," he told NTV.
The train was one of a number of new express trains which came into service last month, offering faster trips between Turkey's two largest cities following renovation on existing tracks. But critics suggested the infrastructure was not suitable for such a project.
"The Turkish railway system has been neglected for the past 50 years. Railway maintenance is insufficient and there are technical deficiencies. In addition, putting fast trains into service carries a risk," Professor Haluk Gercek, an expert on transportation systems at the Istanbul Technical University, told NTV.
The trains travel at speeds of up to 150 kilometres (90 miles) per hour, reducing the duration of the 567-kilometre (352-mile) trip to five hours.
Turkish officials refused to comment on the cause of the accident ahead of a full investigation, but dismissed reports that speeding was the cause.
"We believe that the fact that the train was upgraded to a fast train did not play a role", said Muammer Turker, the head of the railway authority crisis desk.
Asked whether the train might have derailed as a result of sabotage, Turker said: "We have to take into account all possibilities. But I cannot say anything about the cause at the moment, because we do not have any findings."
