Three audio recordings between the control centre in Madrid and two train drivers appear to show that one high-speed train was given clearance to move even though another some 25km (15 miles) up ahead had stalled.
The privately run Iryo train appears to have been stationary on the tracks some distance ahead when the state-run Renfe train barrelled into the back of it at high speed, resulting in the collision.
Hundreds of personnel have been deployed to the disaster site to assist with recovery efforts, according to Spain's interior ministry, with drones and helicopters being used to find victims and remove rubble.
In the first recording, a control centre operator is speaking to the driver of the Renfe train, which was travelling behind the other train and was having some technical difficulties.
The controller tells the driver of the Renfe train to disconnect and reconnect the LZB mechanism that monitors train speeds, and then resume the journey at normal speed.
The Iryo driver then contacts the control centre again, according to a later recording, saying they cannot start the train.
Hospitals in the area suspended planned surgeries as they deal with patients from the crash, Spanish media have reported.
The latter recording suggests that the controller had been notified that the Iryo train remained stationary as the Renfe train approached.