"He has been detained since 7:40pm on Thursday for the alleged crimes of reckless homicide," the minister told reporters in the northwestern city of Santiago de Compostela where the accident happened.
Police said Friday that they had detained the driver, accusing him of "recklessness" in Wednesday night's devastating crash but gave no further details.
They said the driver, identified by media as Francisco Jose Garzon Amo, 52, refused to answer their questions Friday in his hospital bed and the case has been passed to the courts.
The driver will be questioned by a judge on Sunday, the interior minister added.
Under Spanish law, a suspect can be detained for a maximum of 72 hours before being heard by a judge.
"There are reasonable grounds to consider that he may have been responsible for what happened, which must be established by a judge and the investigation which has been opened," he said.
The train was said to have been travelling at more than twice the speed limit on a curve when it hurtled off the rails and slammed into a concrete wall, with one carriage leaping up onto a siding.
The grey-haired driver, who reportedly boasted of his love for speed online, has been under police surveillance in hospital since the accident but he was discharged on Saturday and taken to a police station.
He reportedly suffered head injuries in the accident that required stitches.