News reports say the express train traveling to Ankara derailed at around 1900 (Prague time) on 22 July, nearly two hours after leaving Istanbul.
The accident occurred near the town of Pamukova, about 100 kilometers southeast of Istanbul.
Nearly 40 people were killed, and dozens of others were injured.
Prime Minister Recep Tayyip Erdogan canceled a visit to Bosnia and Herzegovina after news of the accident and traveled overnight to the site of the crash.
Erdogan dismissed earlier death tolls suggesting nearly 140 people had been killed:
"The information we have received from regional hospitals is that, by 0100 [local time], 36 people were killed and another 79 were injured," Erdogan said.
Emergency workers were still looking for survivors in the wreckage by midday on 23 July.
Railways officials say the train was carrying 234 passengers and a nine-member crew.
Before returning to Ankara, the Turkish prime minister said authorities will make a statement once an investigation into the cause of the crash is completed.
Turkey's Anadolu news agency quotes State Railways head Suleyman Karaman as saying on 23 July that sabotage has been ruled out.
Turkish television footage indicates the crash occurred on a straight portion of the track, although the area is reportedly full of turns.
Railways officials believe one of the rear wagons may have derailed first, pulling three other cars off the line.
The five-car train was one of several new express coaches that came into service last month, covering the 570 kilometers that separate Istanbul from Ankara in five hours instead of eight.
The modernization plan has sparked controversy in Turkey, with critics saying the tracks and other infrastructure were too old for trains traveling at up to 150 kilometers per hour on certain portions of the line.
State railway officials, however, say speed is likely not to blame for the crash because the train was traveling at less than 80 kilometers per hour at the time of the accident.
But a surviving passenger indicated the train might have accelerated just before the crash. "I don't really remember all the details. Suddenly, we accelerated. Then dust came up, and we flew through the air for about five seconds. It was very big, like an earthquake," she said.
The accident comes as an embarrassment for Erdogan's government, which has made renovation of Turkey's aging rail network a priority.
In comments made to CNN-Turk, former Transport Minister Oktay Vural blamed the government for ignoring experts' warnings that using the old track was dangerous.
Erdogan skirted the issue on 22 July, saying "these kinds of crashes can happen everywhere in the world."
But Turkish media have been hard on the prime minister and his cabinet.
"Serial Murder" and "High Speed to Massacre" read some of the headlines in national newspapers 23 July, while one editorial in the mass-circulation "Hurriyet" daily called for the resignation of Transport Minister Binali Yildirim.