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Puente announced his decision while addressing lawmakers on Tuesday, November 3, six days after the October 28 crash near Urda, south of Madrid.
He said he had decided to step down within minutes of the latest tragedy but remained in office to oversee the aftermath and introduce measures to prevent similar incidents.
“A transport minister in a country like Spain cannot remain in office after two accidents of this severity in less than a year, however different they may be and regardless of whether or not they bear direct responsibility for them,” he told lawmakers.
He described his resignation as “a matter of political dignity, consistency and political empathy” but did not specify when he would formally leave office.
The October 28 collision occurred when a high-speed train operated by state-owned Renfe crashed into the rear of a stationary Iryo train on the Madrid-Andalusia line. More than 200 people were injured in the incident.
Authorities have attributed the crash to a combination of human and computer failures. Puente had earlier told lawmakers that a red signal had prohibited movement, yet the train was authorised to proceed.
The outgoing minister also confirmed that he would not seek a seat in Spain’s early general election scheduled for November 29.
His resignation comes amid public pressure following the crash, with demonstrators calling for political accountability. However, trade union representatives have questioned attempts to place the blame primarily on individual workers, arguing that failures in the railway safety system must also be investigated.
