The train collided with four people who were on the tracks at around 6am on Tuesday in Ciboure, a short distance from the station of the coastal town of Saint-Jean-de-Luz.
Three died at the scene while the fourth is in critical condition and has been taken to hospital, French news channel BFMTV reported.
According to the public prosecutor of Bayonne, Jérôme Bourrier, who was on the scene on Tuesday morning, all four victims were migrants, RTL reported.
The four were lying down on the tracks at the moment of the accident, police sources told BFM TV.
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Police have opened an investigation into the circumstances of the accident and to determine why the individuals were on the track at the time.
The train had begun in Hendaye close to the Spanish border and was making its way towards Bordeaux.
Services on the line between Hendaye and Bayonne were initially suspended, but trains began running again shortly after 8am.
“Trains will nevertheless have to advance carefully near Saint-Jean-de-Luz,” TER Nouvelle-Aquitaine tweeted.
🟠8h17 : l'intervention des équipes spécialisées est terminée, la circulation #Bordeaux ➡ #Hendaye peut reprendre progressivement.
Les trains devront néanmoins circuler prudemment près de #Saint_Jean_de_Luz.
Je suis toujours à votre disposition pour vos questions 💬 https://t.co/3h5q1dxROE
— TER NVELLE-AQUITAINE 🎀 (@TERNouvelleAQ) October 12, 2021