Three train drivers were among the nine killed in the crash, Transport Minister Cahit Turhan told reporters on the scene.
Turkish authorities detained three railway agency employees suspected of negligence over the high-speed train crash in Ankara which killed at least nine people and injured 47 others.
Ankara governor Vasip Sahin had earlier said four people had died and 43 were injured.
In November, at least 15 people were injured when a passenger train collided with a freight train in Turkey's central province of Sivas.
Parts of the overpass at Marsandiz station collapsed onto the train.
The head-on collision between the high-speed train and the pilot engine, which was returning from checking the rails, occurred around six minutes after the first' departure from Ankara terminal at 06.30 (0330GMT), Turhan added.
It wasn't immediately clear if a signaling problem caused the crash.
This image made from video shows aftermath of a high-speed train crash at a station in Ankara Turkey Thursday Dec. 13 2018
He said, search and rescue efforts are underway and technical investigations have begun to ascertain what caused the accident.
The accident occurred at about 6:30am Thursday, local time, at the Marsandiz railway station, around eight kilometres from Ankara's main station. The locomotive, which was being used to carry out track inspections, derailed.
The windows of one wagon were completely broken while another wagon had been smashed after hitting the footbridge, which also collapsed, an AFP correspondent at the scene said.
Turkey has suffered a number of train crashes in recent months.
According to Anadolu, 206 passengers were on the train at the time of the crash. In July, 24 people were killed after a train derailed en route to Istanbul.
Turkey has been steadily expanding its high-speed rail network, and there are several mega infrastructure projects planned in the lead up to 2023, when the country marks 100 years since the founding of the modern republic.