The Spanish doctor was given a one year jail sentence on Tuesday after being found guilty of helping cyclists to carry out blood transfusions.
The jail term was given several years after police found the blood bags at his Madrid laboratories, although the judge has since ordered the packs to be destroyed rather than be DNA tested.
Murray took to his Twitter account to voice his disapproval of the outcome.
"operacion puerto case is beyond a joke..." tweeted the British number one.
"biggest cover up in sports history? why would court order blood bags to be destroyed? #coverup"
The World Anti-Doping Agency are still hoping to overturn the decision on appeal.