"Instead of preparations for the Euro 2012, I will have an operation on my shoulder joint ligaments and undergo rehabilitation," the Dynamo Kiev keeper was quoted as saying by his club's website.
"The most important thing is for the operation to be a success. I expect my rehabilitation to take three months."
The 37-year-old's absence will be a major blow for the side who face England, France and Sweden in Group D of the month-long tournament being co-hosted by Ukraine and Poland.
Renowned for his penalty saving ability, Shovkovsky, who has 92 caps, became the first goalkeeper in World Cup history not to concede a goal during a penalty shootout at the Germany tournament in 2006.
Ukraine will now go into the tournament with a shortage of experienced keepers after Oleksandr Rybka was suspended for using a banned diuretic and Andriy Dykan looks set to miss the finals after picking up a serious injury in March.
"I am desperate to be fit enough for the Euro 2012 tournament but time is passing and I understand that my dreams of playing are vanishing," he was quoted as saying last week.