Quintana was leading the overall standings heading into Tuesday's 10th-stage time trial but a spectacular high-speed tumble led to him dropping down to 11th, nearly 3-1/2 minutes behind Spaniard Alberto Contador, who took over the leader's red jersey.
Quintana "feels pain in his right-hand shoulder and has been moved by ambulance to a medical center to check on any fractures," Movistar said on their Twitter feed.
The Giro d'Italia winner had "suffered a displaced fracture in his right-hand scapula" and would "undergo surgery on Thursday", the team added in a later post.
The incident happened around the 20-km mark of Wednesday's 153.4-km stage, which started in Pamplona and finishes with a steep climb to San Miguel de Aralar.
(Reporting by Iain Rogers, editing by Justin Palmer/Rex Gowar)
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