The two trains crashed head-on near the town of Gebze, southeast of Istanbul, after one ran a red light, officials said.
But experts were quick to blame the accident on a possible error in the decade-old signalling system and on technical failures.
The government had already come under fire after a newly inaugurated express train derailed in the same region in the northwest, killing 37 people and leaving some 80 others injured, on 22 July.
The new service was launched despite warnings that the country's ageing tracks would not withstand high speeds.
Newspapers are wondering if the
railway system has collapsed
"Are you going to continue sitting in those armchairs of yours?" the Radikal newspaper said on Thursday in an angry appeal to officials on its front page.
"The government did not hear the warnings," Cumhuriyet said, while Aksam described the crash as a "painful indication of the collapse of the railway system".
Officials insisted that the signalling system was functioning properly, but one of the train drivers who survived the crash cast doubt on the claim.
Interviewed in hospital, with both arms broken, Hasan Yucedag told Anatolia news agency the signal had been green as his train approached.
"But suddenly the signal changed to red. The other train was at a stop. I don't know how it happened. The light turned red. I don't remember anything after that," he said.
"... suddenly the signal changed to red. The other train was at a stop. I don't know how it happened. The light turned red. I don't remember anything
Driver of one train who survived the collision
Some experts also suggested that the trains were not equipped with an automatic braking system which would have stopped the train in case of a driver's mistake.
The two trains crashed head-on, hurling one carriage off the tracks.
One of the trains was en route from Ankara to Istanbul with 153 passengers and nine staff on board. The other one was heading from Istanbul to the city of Adapazari, also in the northwest.