"Obtaining the blood bags provides additional elements which could be used as evidence in disciplinary proceedings," UCI spokeswoman Devra Pitt Getaz told The Associated Press in an email.
Unless overturned, the ruling prevents officials from identifying the doctor's blood-doping clients and pursuing disciplinary cases against them. Fuentes admitted having clients from cycling, tennis, soccer and boxing, but has not revealed their identities.
The Madrid court found Fuentes guilty of endangering public health and handed him a one-year suspended jail sentence. He was barred from sports medical practice for four years and ordered to pay a $6,000 fine.
Judge Julia Santamaria cited Spanish privacy laws in her decision not to turn over the evidence to anti-doping authorities.
The UCI said it will appeal to a Madrid appeals court.
More than 50 cyclists were implicated in the Puerto investigation, with Italian rider Ivan Basso and Alejandro Valverde of Spain among those banned for involvement in the case.
The World Anti-Doping Agency and Spanish national anti-doping agency also have said they were considering appeals. The deadline for appeals is May 17.
WADA director general David Howman said last month the court ruling was "particularly disappointing and unsatisfactory."
The International Olympic Committee has long called for all the Puerto evidence to be turned over.