The announcement comes 10 years after Operation Puerto revealed a doping network involving some of the world`s top cyclists.
Police seized 211 coded blood bags from the clinic of Dr Eufemiano Fuentes.
They must now be given to the World Anti-Doping Agency, cycling bosses and the Italian Olympic Committee.
The authorities successfully appealed against a decision three years ago to destroy the blood bags.
More than 50 cyclists were originally linked to the case.
Among those eventually suspended were former Tour de France winner Jan Ullrich, Spanish Vuelta champion Alejandro Valverde and Ivan Basso, who later confirmed that his blood was among the frozen samples found.
Fuentes also worked in other sports and the new ruling raises the potential for the identities of additional athletes to be revealed.
The sports doctor was given a suspended one-year prison sentence for endangering public health, but that sentence was later overturned.
Ten years ago, police seized the blood bags from the Madrid clinic of Fuentes as part of Operation Puerto.
The bags belonged to athletes who received treatments from the doctor, though he has refused to confirm whether the anonymous athletes were doping or not.
In April 2013, Judge Julia Patricia Santamaria ruled the blood bags should be destroyed, a decision which provoked widespread criticism.
Since then, the bags have been stored in an anti-doping laboratory in Barcelona.
Blood bags in Spanish cycling doping case to be handed over
14 June 2016
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Blood bags used as evidence in a major Spanish doping scandal must be handed over to authorities for investigation, a Madrid court has ruled.
