The 35-year-old Italian rider gave the sample during an out-of-competition test in March 2012, the UCI said in a statement.
The retest came as a result of the UCI's storage and reanalysis policy which banks samples from the leaders of the Grand Tours, UCI World Championships and "general rankings" of all cycling disciplines for up to 10 years.
"The Union Cycliste Internationale (UCI) announces that it has notified Italian rider Giampaolo Caruso of an Adverse Analytical Finding of Erythropoietin (EPO) in a sample collected during an out-of-competition test on 27 March 2012. The sample had been stored and was reanalysed in light of new scientific developments," the UCI said in a statement.
Caruso has the right to request analysis of his B sample. His Katusha team said the news came as a "complete shock" but that it would wait for the final results before making a decision on the rider.
Caruso is the second Katusha rider to be suspended this season after Luca Paolini tested positive for cocaine during the Tour de France but the team is in no danger of suspension this season because the retested sample is from 2012.
This not the first time Caruso has been implicated in doping. He tested positive for nandrolone after winning the Willunga Hill stage at the 2003 Tour Down Under and was later suspended for six months and fined.
He was also caught up in the infamous Operación Puerto case, but was acquitted of involvement by the Court for Arbitration for Sport (CAS) despite demands for a two-year suspension by the Italian Olympic Committee.