Spanish doctor Eufemiano Fuentes, the central figure in the trial, was given a one-year prison term for endangering public health and the judge also ordered the evidence, including bags of blood possibly belonging to athletes from sports other than cycling, to be destroyed.
Her decision not to release evidence to anti-doping authorities for further investigation damaged hopes that the case would unmask other athletes involved in illegal doping, and prompted widespread condemnation.
"WADA has carefully considered the decision rendered by the Criminal Court in Madrid in relation with the Operation Puerto," the agency's director general, David Howman, said in a statement on the agency's website.
"The decision to order the destruction of all the blood bags is particularly disappointing and unsatisfactory for WADA, and the whole anti-doping community," Howman added.
"Access to this evidence motivated WADA's involvement in this case.
"This would ensure appropriate sports sanction processes against the cheats who used Dr Fuentes's services."
The Spanish anti-doping agency (AEA) has already said it will appeal against the judge's ruling to destroy the evidence and Howman said WADA might follow suit.
"WADA is currently fully reviewing the decision and any possible appeal or other action with its Spanish legal advisors, and the Spanish National Anti-Doping Organisation (AEA)," he said, adding that the appeal deadline was May 17.
WADA, the AEA, the Spanish cycling federation (RFEC), the International Cycling Union (UCI) and the Italian Olympic Committee (CONI) were all represented in the three-month trial in Madrid.
Fuentes, who denied doping, said in his opening testimony that he had clients in cycling but also in sports including soccer, tennis, athletics and boxing.
Spain has been hoping the trial will help to dispel the impression that the nation was soft on doping and boost Madrid's bid to win the right to host the 2020 Olympic Games.
The country is pushing updated anti-doping legislation through parliament which the government says will bring Spain into line with international norms.
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- Eufemiano Fuentes