He announced his decision in Congress, where he had appeared to give the circumstances of last Wednesday’s crash near the town of Urda, south of the capital Madrid, BBC reported.
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“A transport minister in a country like Spain cannot remain in office after two accidents of this seriousness in less than a year,” he said, also referring to a deadly crash in January in Andalusia, southern Spain.
The latest tragedy in Urda happened when a state-operated Renfe high-speed train smashed into the back of another stationary train operated by the Iryo company.
Puente announced his decision at the end of a congressional session in which he had outlined new rail safety measures and been grilled by the opposition.
He said he had taken the decision immediately after the 28 October disaster – but but had waited several days before announcing it.
Puente had been under mounting pressure as opposition parties and some allies of the government called on him to step down.
Leaked audio recordings published in Spanish media soon after the crashed revealed conversations between train drivers and a control centre just minutes before the disaster.
Prime Minister Pedro Sánchez has said that authorities will “get to the bottom of every last detail of this tragedy”.
