Armed troops were guarding the site. By nightfall, rescue operations had largely ended and emergency crews were using flashlights to search inside the wreckage for any bodies.
The accident occurred after a train traveling from Ankara to Istanbul ignored a signal and failed to stop at a junction, Cemal Yaman, an official of a local branch of the train workers' union told the Anatolia news agency. The train was carrying 153 passengers and nine crew members.
Deputy Prime Minister Abdullah Gul said, ''One of the trains passed a red light. When the [engineer] noticed he tried to reduce speed but unfortunately the accident occurred."
However, conductor Hasan Yucedag told Anatolia from his hospital bed that ''the light was green for us. It suddenly turned red as we were about to cross." Yucedag suffered a broken arm.
The other train was traveling from Istanbul to Adapazari in northwestern Turkey, officials said.
The prime minister's office said six people were killed and 85 were injured. Most of the injured were released from the hospital by nightfall.
Mahmut Yanmis, who survived the accident, told CNN-Turk television the collision occurred after his train left Tavsancil station.
''I made my way through a broken window," said Yanmis, who had stitches on his head and scratches on his arms.
The accident happened three weeks after a new high-speed train from Istanbul to Ankara derailed, killing 37 people -- one of the worst train accidents in Turkey.
Three days after the derailment, a passenger train slammed into a minibus at a western railroad crossing, killing 15 people and injuring four others.