There was a mass crash with 200 metres to go, in the midst of the mass sprint. Fernandez suffered cuts and concussion and was taken to hospital.
Such a head injury requires the patient to remain 24 hours in hospital for observation, the team said on its website.
In Thursday's stage, Fernandez' teammate Ruben Perez Moreno lost the overall lead to HTC-Columbia's young Australian Leigh Howard, on bonus seconds. The sprint was won by Robert Wagner of Skil-Shimano, with Howard finishing second.
Fernandez, 28, most recently finished second in the Tour de Picardie. He has been with the Basque team since 2004.
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