"He said he was not talking at the moment the train left the tracks, but that he had hung up a few seconds beforehand," the court said in a statement, after the driver Francisco Jose Garzon Amo testified to the judge for a second time on Wednesday.
Judge Luis Alaez has released Garzon on bail charged with 79 counts of reckless homicide, while the court investigates.
With 79 people killed and 178 injured, it was Spain's worst rail disaster since 1944.
Garzon had said in his first testimony to the Galicia regional court on Sunday that he "didn't understand" how he failed to brake in time, a recording of his court hearing revealed.
"I can't explain. I still don't understand," the driver told the judge when asked why he hadn't slowed down in time to take a sharp bend near the northwestern city of Santiago de Compostela.
Asked again about what caused him to crash, he added: "I tell you sincerely that I don't know. Otherwise I would not have been so crazy as not to brake" earlier.
That first testimony, made during a closed-door hearing on Sunday, was recorded and an extract posted online by leading newspaper El Pais.
Railway officials say the track where the train crashed was not equipped with the automatic braking systems in place on some high-speed lines and that it was therefore left up to the driver to brake.
The driver told the judge he had braked, but by the time he did so the crash was "inevitable".
"Before the train turned over, I had activated everything but I saw that no, no, it wasn't working."
The black box data recorders revealed the train was going at 192 kilometres (119 miles) per hour before braking shortly before the bend.
When it derailed it was travelling at 153kph — nearly twice the 80kph speed limit on that part of the line.
Garzon identified the person he was talking to on the telephone as a conductor of the state rail company Renfe who was on the train, the court said.
Spain's El Pais newspaper later quoted the conductor, whom it named as Antonio Martin Marugan, as saying he had called Garzon on his work telephone to advise him on which platform to use at a later stop.
The daily cited sources closing to the investigation as saying they believed Martín had chosen not to reveal details of this call earlier to protect the driver.
This is because Renfe drivers are only permitted to speak on the company phone while driving in "exceptional circumstances".
Those same sources said Garzón may have forgotten the details of this call with the conductor because he was in a state of shock after the accident.
Martin said he and Garzon were good friends, according to the newspaper.
The court said Garzon had returned voluntarily on Wednesday to testify to the judge about the phone call, after his first hearing on Sunday.