Fuentes, the central figure in the Operation Puerto case, a drugs scandal with possible repercussions across all sports, was sentenced to a year in prison - but the judge presiding over the case also ruled that all evidence in the case was to be destroyed, damaging the chances of understanding the operation's scale and breath.
Fuentes - who is unlikely to be jailed because sentences under two years in Spain are usually suspended - was convicted for crimes against public health, barred from practising sports medicine for four years and fined.
However, judge Julia Santamaria's decision not to release case evidence, including bags of blood seized in police raids, to anti-doping authorities for further investigations hit hopes that the case would unmask athletes caught up in the doping programme.
Murray, writing on Twitter, asked whether the verdict represented the biggest cover-up in sports history.
"operacion puerto case is beyond a joke... biggest cover up in sports history? why would court order blood bags to be destroyed? #coverup"
The Spanish anti-doping agency has said that it would appeal the judge's ruling to destroy the evidence.